bluuebunny/crossref_metadata_2025 huggingface dataset:
Adenovirus origin of DNA replication: sequence requirements for replication in vitro.
Authors: Wides R J , Challberg M D , Rawlins D R , Kelly T J
Published: September 2015

The initiation of adenovirus DNA takes place at the termini of the viral genome and requires the presence of specific nucleotide sequence elements. To define the sequence organization of the viral origin, we tested a large number of deletion, insertion, and base substitution mutants for their ability to support initiation and replication in vitro. The data demonstrate that the origin consists of at least three functionally distinct domains, A, B, and C. Domain A (nucleotides 1 to 18) contains the minimal sequence sufficient for origin function. Domains B (nucleotides 19 to 40) and C (nucleotides 41 to 51) contain accessory sequences that significantly increase the activity of the minimal origin. The presence of domain B increases the efficiency of initiation by more than 10-fold in vitro, and the presence of domains B and C increases the efficiency of initiation by more than 30-fold. Mutations that alter the distance between the minimal origin and the accessory domains by one or two base pairs dramatically decrease initiation efficiency. This critical spacing requirement suggests that there are specific interactions between the factors that recognize the two regions.
Structure of the rat platelet factor 4 gene: a marker for megakaryocyte differentiation.
Authors: Doi T , Greenberg S M , Rosenberg R D
Published: September 2015

A rat platelet factor 4 (PF4) cDNA has been isolated by immunoscreening a g lambda 11 rat megakaryocyte cDNA expression library. Sequence analysis of the rat PF4 cDNA revealed that this megakaryocyte protein is composed of a leader sequence of 29 amino acid residues and a mature protein sequence of 76 amino acid residues. The structure of rat PF4 derived from its cDNA shows a marked homology with the amino acid sequence of human PF4 obtained by classical protein chemistry techniques. This observation is particularly striking with regard to the carboxy-terminal region of rat and human PF4, where 28 of the last 31 C-terminal residues are identical. The rat PF4 gene was obtained from a rat genomic library by using rat PF4 cDNA as a hybridization probe. Sequence analysis showed that the gene is constructed of three exons and two short introns. The transcriptional start site is located 73 base pairs upstream of the translational start codon as judged by S1 nuclease mapping and primer extension. The 5' noncoding region of the gene also exhibited a sequence homologous to the TATA box at -31, as well as a series of direct and inverted repeat sequences and a cluster of 26 T residues at -155 to -218. This latter domain may be involved in regulating PF4 gene expression during megakaryocytopoiesis.
Activation of c-myc and c-K-ras oncogenes in primary rat tumors induced by ionizing radiation.
Authors: Sawey M J , Hood A T , Burns F J , Garte S J
Published: September 2015

An activated K-ras oncogene was detected by transfection in NIH 3T3 cells and by Southern blot analysis in 6 of 12 rat skin tumors induced by ionizing radiation. The DNA from 10 of the 12 tumors also showed c-myc gene amplification and restriction polymorphisms. Evidence for tissue specificity was observed in patterns of oncogene activation, with each of three clear cell carcinomas exhibiting activation of both c-myc and K-ras oncogenes.
Presence of a c-myc transcript initiated in intron 1 in Friend erythroleukemia cells and in other murine cell types with no evidence of c-myc gene rearrangement.
Authors: Ray D , Meneceur P , Tavitian A , Robert-Lezenes J
Published: September 2015

In Friend murine erythroleukemia cells, although no detectable c-myc gene rearrangement was found, we observed, in addition to the normal 2.3-kilobase c-myc transcript, the presence of a 2.3-kilobase c-myc mRNA initiated in intron 1 at a promoter site called P3. The intron 1-initiated transcript has a longer half-life than the normal c-myc mRNA. This c-myc transcript initiated in intron 1 was also found in other murine cell types where no rearrangement of the c-myc locus has been reported.
Polyomavirus middle T antigen downregulates junctional cell-to-cell communication.
Authors: Azarnia R , Loewenstein W R
Published: September 2015

We examined the effect of polyomavirus middle T antigen on cell-to-cell communication in rat F cells transfected with an inducible middle T recombinant DNA or infected with a conditional mutant virus. Junctional permeability fell (reversibly) when middle T transcription was induced or when middle T was switched to the transformation+ form. The effect correlates with the rise of protein tyrosine kinase activity.
Nucleotide sequence and functional analysis of the RAD1 gene of Saccharomyces cerevisiae.
Authors: Reynolds P , Prakash L , Prakash S
Published: September 2015

The RAD1 gene of Saccharomyces cerevisiae is involved in excision repair of damaged DNA. The nucleotide sequence of the RAD1 gene presented here shows an open reading frame of 3,300 nucleotides. Two ATG codons occur in the open reading frame at positions +1 and +334, respectively. Since a deletion of about 2.7 kilobases of DNA from the 5' region of the RAD1 gene, which also deletes the +1 ATG and 11 additional codons in the RAD1 open reading frame, partially complements UV sensitivity of a rad1 delta mutant, we examined the role of the +1 ATG and +334 ATG codons in translation initiation of RAD1 protein. Mutation of the +1 ATG codon to ATC affected the complementation ability of the RAD1 gene, whereas mutation of the +334 ATG codon to ATC showed no discernible effect on RAD1 function. These results indicate that translation of RAD1 protein is initiated from the +1 ATG codon. Productive in-frame RAD1-lacZ fusions showed that the RAD1 open reading frame is expressed in yeasts. The RAD1-encoded protein contains 1,100 amino acids with a molecular weight of 126,360.
Multiple proteins bind to VA RNA genes of adenovirus type 2.
Authors: Van Dyke M W , Roeder R G
Published: September 2015

Using fractionated HeLa cell nuclear extracts and both nuclease (DNase I) cleavage and chemical cleavage (methidiumpropyl-EDTA X Fe(II) protection methodologies, we demonstrated the presence of three proteins which interacted specifically, yet differentially, with the two VA genes of adenovirus type 2. One, previously identified as transcription initiation factor TFIIIC, bound to a site centered on the transcriptionally essential B-block concensus element of the VAI gene and, with a lower affinity, to the analogous site in the VAII gene. Another, identified as the cellular protein involved in adenovirus replication, nuclear factor I, bound to sites immediately downstream from the two VAI terminators (at approximately +160 and +200). The third, a previously unrecognized VA gene binding protein termed VBP, bound immediately upstream of the B-block element in the VAI gene but showed no binding to VAII. Possible roles for these proteins in VA gene transcription were investigated in in vitro assay systems reconstituted with partially purified transcription factors (RNA polymerase III, TFIIIB, and TFIIIC). Although TFIIIC activity was present predominantly in fractions containing B-block binding activity, there was not complete correspondence between functional and DNA binding activities. The nuclear factor I-like protein had no effect when added to a complete transcription reaction. The presence of VBP appeared to depress the intrinsic ratio of VAI-VAII synthesis, thereby simulating the relative transcription levels observed early in adenovirus infection of HeLa cells. These observations suggest a model, involving both intragenic binding factors (VBP and TFIIIC) and variable template concentrations, for the differential regulation of VA transcription during the course of adenovirus infection.
Organization of the Drosophila melanogaster hsp70 heat shock regulation unit.
Authors: Amin J , Mestril R , Schiller P , Dreano M , Voellmy R
Published: September 2015

Expression from the Drosophila melanogaster hsp70 promoter was controlled by a regulatory unit that was composed of two sequence elements that resembled the heat shock consensus sequence. The unit functioned in both orientations and at different distances from downstream promoter sequences. Each element of the unit alone was essentially inactive. Association of two elements resulted in a dramatic increase of transcription from the hsp70 promoter. This synergistic effect was independent of the relative orientation of the elements and, to a large extent, of the distance between them. Duplication of a region containing only one element also yielded a highly active, heat-regulated promoter. Genes with three to five elements were three to four times more active than those with a single regulatory unit.
Rapid inhibition of processing and assembly of small nuclear ribonucleoproteins after infection with vesicular stomatitis virus.
Authors: Fresco L D , Kurilla M G , Keene J D
Published: September 2015

After infection of baby hamster kidney cells with vesicular stomatitis virus (VSV), processing and assembly of small nuclear ribonucleoproteins (snRNP) were rapidly inhibited. The U1 and U2 snRNAs accumulated as precursor species approximately 3 and 10 nucleotides longer, respectively, than the mature RNAs. Alteration in snRNP assembly was noted because the precursor snRNAs were not associated with the U-series RNA-core protein complex in infected cells. However, antibodies specific for the U2 RNA-binding protein, A', were able to precipitate pre-U2 RNAs from VSV-infected cells. These results indicated that precursors to U2 RNA were bound to A' and remained bound during virus infection. Analysis of the synthesis of proteins normally associated with U1 and U2 RNAs indicated that synthesis was unaffected at times when snRNP assembly with core proteins was blocked by the VSV. These findings suggested that the core proteins associate with one another in the absence of the snRNAs in VSV-infected cells. They further suggest a correlation between the inability of the core complex to bind the U-series snRNPs and the failure to process the 3' ends of U1 and U2 RNAs in VSV-infected cells. These effects of VSV on snRNP assembly may be related to the shutoff of host-cell macromolecular synthesis.
Repression of insulin gene expression by adenovirus type 5 E1a proteins.
Authors: Stein R W , Ziff E B
Published: September 2015

Insulin gene transcription relies on enhancer and promoter elements which are active in pancreatic beta cells. We showed that adenovirus type 5 infection of HIT T-15 cells, a transformed hamster beta cell line, represses insulin gene transcription and mRNA levels. Using expression plasmids transiently introduced into HIT T-15 cells, we showed that adenovirus type 5 E1a transcription regulatory proteins repress insulin enhancer-promoter element activity as assayed with a surrogate xanthine-guanine phosphoribosyltransferase gene. We relate E1a repression of the insulin gene to other examples of repression of enhancer-dependent genes by E1a and discuss the possible relationship of this repression to insulin gene regulation.
RAD4 gene of Saccharomyces cerevisiae: molecular cloning and partial characterization of a gene that is inactivated in Escherichia coli.
Authors: Fleer R , Nicolet C M , Pure G A , Friedberg E C
Published: September 2015

In contrast to other Saccharomyces cerevisiae RAD genes involved in nucleotide excision repair of DNA, the RAD4 gene could not be isolated by screening a yeast genomic library for recombinant plasmids which complement the UV sensitivity of rad4 mutants (Pure et al., J. Mol. Biol. 183:31-42, 1985). We therefore attempted to walk to RAD4 from the neighboring SPT2 gene and obtained an integrating derivative of a plasmid isolated by Roeder et al. (Mol. Cell. Biol. 5:1543-1553, 1985) which contains a 4-kilobase fragment of yeast DNA including a mutant allele of SPT2. When integrated into several different rad4 mutant strains, this plasmid (pR169) complements UV sensitivity at a frequency of approximately 10%. However, a centromeric plasmid containing rescued sequences which include flanking yeast DNA no longer complements the phenotype of rad4 mutants. Complementing activity was restored by in vivo repair of a defined gap in the centromeric plasmid. The repaired plasmid fully complements the UV sensitivity of all rad4 mutants tested when isolated directly from yeast cells, but when this plasmid is propagated in Escherichia coli complementing activity is lost. We have mapped the physical location of the RAD4 gene by insertional mutagenesis and by transcript mapping. The gene is approximately 2.3 kilobases in size and is located immediately upstream of the SPT2 gene. Both genes are transcribed in the same direction. RAD4 is not an essential gene, and no increased transcription of this gene is observed in cells exposed to the DNA-damaging agent 4-nitroquinoline-1-oxide. The site of inactivation of RAD4 in a particular plasmid propagated in E. coli was localized to a 100-base-pair region by gene disruption and gap repair experiments. In addition, we have identified the approximate locations of the chromosomal rad4-2, rad4-3, and rad4-4 mutations.
Interaction of a tissue-specific factor with an essential rat growth hormone gene promoter element.
Authors: West B L , Catanzaro D F , Mellon S H , Cattini P A , Baxter J D , Reudelhuber T L
Published: September 2015

Rat growth hormone (rGH) gene expression is normally restricted to the anterior pituitary. As a model of this tissue specificity, we compared the transient expression of an rGH-chloramphenicol acetyltransferase (CAT) hybrid gene in rGH-producing rat pituitary tumor (GC) cells and in non-rGH-producing rat fibroblast (rat-2) cells. Deletion analysis of the rGH portion of this hybrid gene demonstrated that DNA sequences within 140 base pairs 5' to the rGH gene were sufficient for correct cell type-specific expression. Deletion of an additional 35 base pairs of the rGH 5'-flanking DNA resulted in a loss of expression of the transfected hybrid gene and correlated with the interaction of a putative trans-acting factor with this region of the rGH promoter. This factor was detectable by DNase I footprinting in a crude nuclear extract from GC cells but not from rat-2 cells. Site-directed mutagenesis of the footprint region caused complete loss of expression of a hybrid gene containing 530 base pairs 5' to the rGH gene. Thus, the interaction of this factor, which we term GC2, is likely to be essential for the tissue-specific expression of the rGH gene.
Insulin induction of Xenopus laevis oocyte maturation is inhibited by monoclonal antibody against p21 ras proteins.
Authors: Deshpande A K , Kung H F
Published: September 2015

Microinjection of transforming p21 ras protein induces maturation of Xenopus laevis oocytes, and the induction is blocked by coinjection of monoclonal antibody (Y13-259) against p21 ras proteins. Similar to other inducing agents, the effect of p21 ras protein is mediated via the appearance of maturation or meiosis-promoting factor activity. In addition, the neutralizing antibody markedly reduces oocyte maturation after insulin induction, whereas it fails to inhibit progesterone induction. Our results suggest that insulin induces maturation of oocytes via a different pathway than that of steroidal agents. The induction by insulin is ras dependent, and the action of ras may be directed at the steps before meiosis-promoting factor autocatalytic activation. These results suggest a role of p21 ras protein in the events associated with amphibian oocyte maturation.
Human ribosomal DNA fragments amplified in hamster cells are transcribed only by RNA polymerase II and are not silver stained.
Authors: Dhar V N , Miller D A , Kulkarni A B , Miller O J
Published: September 2015

Cloned human rRNA gene fragments that included the promoter region were introduced into Chinese hamster dihydrofolate reductase-deficient (dhfr-) cells by cotransformation with a dhfr minigene and amplified by selection for methotrexate resistance. The human ribosomal DNA was transcribed by RNA polymerase II, not RNA polymerase I or III. The metaphase chromosome regions containing the transcriptionally active human ribosomal DNA failed to show silver staining.
The ovarian, ecdysterone, and heat-shock-responsive promoters of the Drosophila melanogaster hsp27 gene react very differently to perturbations of DNA sequence.
Authors: Hoffman E P , Gerring S L , Corces V G
Published: September 2015

The effect of various types of DNA sequence alterations on the activity of the ovarian, ecdysterone, and heat-shock-responsive promoters of the Drosophila melanogaster hsp27 gene was studied by P element-mediated germ line transformation. Regions of DNA required for proper expression of the gene under these different conditions were identified. Wild-type levels of transcription during oogenesis are dependent on two elements respectively located within a 64-base-pair (bp) fragment in the transcribed untranslated region and between -227 and -958 bp upstream of the transcription start site. This ovarian expression is particularly sensitive to both chromosomal position effects and an increased distance between the distal upstream promoter element and the TATAA homology. The ecdysterone-mediated expression during metamorphosis is dependent on a 145-bp domain including the TATAA box and additional upstream sequences that augment transcription by two- to five-fold. Finally, sequences necessary for heat shock expression are located much further upstream from hsp27 than those previously found for hsp70, although basal expression was correlated with the presence of more proximal heat shock consensus sequences.
Positive regulation of the beta-galactosidase gene from Kluyveromyces lactis is mediated by an upstream activation site that shows homology to the GAL upstream activation site of Saccharomyces cerevisiae.
Authors: Ruzzi M , Breunig K D , Ficca A G , Hollenberg C P
Published: September 2015

In contrast to the Escherichia coli lac operon, the yeast beta-galactosidase gene is positively regulated. In the 5'-noncoding region of the Kluyveromyces lactis LAC4 gene, we mapped an upstream activation site (UAS) that is required for induction. This sequence, located between positions -435 and -326 from the start of translation, functions irrespective of its orientation and can confer lactose regulation to the heterologous CYC1 promoter. It is composed of at least two subsequences that must act in concert. One of these subsequences showed a strong homology to the UAS consensus sequence of the Saccharomyces cerevisiae GAL genes (E. Giniger, S. M. Varnum, and M. Ptashne, Cell 40:767-774, 1985). We propose that this region of homology located at about position -426 is a binding site for the product of the regulatory gene LAC9 which probably induces transcription of the LAC4 gene in a manner analogous to that of the GAL4 protein.
Adeno-associated virus gene expression inhibits cellular transformation by heterologous genes.
Authors: Labow M A , Graf L H , Berns K I
Published: September 2015

In this paper we report that adeno-associated virus (AAV) genomes inhibit stable transformation by several dominant selectable marker genes upon cotransfection into mouse tissue culture cells. Cotransfection of AAV genomes also inhibited the expression of pSV2cat in transient assays. In both cases, the inhibitory effect was independent of AAV DNA replication but required the AAV p5 and p19 genes, which encode proteins required for AAV DNA replication and regulation of AAV gene expression. Finally, addition of a cloned E4 gene in the transfection experiments partially blocked the AAV-mediated inhibitory activities.
In vitro splicing of kappa immunoglobulin precursor mRNA.
Authors: Lowery D E , Van Ness B G
Published: September 2015

The in vitro splicing of kappa immunoglobulin precursor mRNA was studied as an example of a naturally occurring mRNA possessing multiple 5' splice sites. Several kappa mRNAs were generated in vitro by using an SP6 transcription system and were spliced in nuclear extracts derived from HeLa cells. Products and intermediates resulting from in vitro splicing were identified and characterized. In contrast to the in vivo situation, in which apparently only the 5'-most splice donor site is used, all of the 5' splice sites were used in vitro with equal frequency. Neither the presence or absence of variable region coding sequences nor the deletion of intron sequences had an effect on in vitro splice site selection.
Metallothionein gene expression is regulated by serum factors and activators of protein kinase C.
Authors: Imbra R J , Karin M
Published: September 2015

The exact physiological role of metallothionein (MT) is not clear. It has been suggested that these low-molecular-weight, highly inducible, heavy-metal-binding proteins serve in the regulation of intracellular Zn metabolism. Among the Zn-requiring systems are several enzymes involved in DNA replication and repair. Therefore, during periods of active DNA synthesis there is likely to be an increased demand for Zn, which could be met by elevated MT synthesis. For that reason, we examined whether stimulation of cellular proliferation leads to increased expression of MT. We report here that treatment of cultured mammalian cells with serum growth factors and activators of protein kinase C, all of which are known to have growth stimulatory activity, led to induction of MT mRNA. One of the required steps in the signal transduction pathways triggered by these agents, ending in MT induction, appears to be the activation of protein kinase C.
Interruption of two immunoglobulin heavy-chain switch regions in murine plasmacytoma P3.26Bu4 by insertion of retroviruslike element ETn.
Authors: Shell B , Szurek P , Dunnick W
Published: September 2015

A number of moderately reiterated murine genetic elements have been shown to have structures like those of retroviral proviruses. These elements are thought to be transposons, although little evidence of their transposability exists. Two members of one of these families of reiterated elements, the ETn family, have inserted into separate immunoglobulin heavy-chain switch regions in the plasmacytoma P3.26Bu4. Switch regions are those DNA segments associated with each immunoglobulin heavy-chain gene in which the somatic recombinations that accompany the heavy-chain switch occur. This role in somatic recombination may be relevant to the ETn insertions into the switch regions in P3.26Bu4 DNA. P3.26Bu4 and a number of other B-lineage cells contain ETn transcripts.
ret transforming gene encodes a fusion protein homologous to tyrosine kinases.
Authors: Takahashi M , Cooper G M
Published: September 2015

The ret transforming gene was activated by recombination between two unlinked segments of human DNA, most likely during transfection of NIH 3T3 cells. To further define this transforming gene, we isolated and sequenced ret cDNA clones. The nucleotide sequence indicates that the active ret transforming gene encodes a fusion protein with a carboxy-terminal domain which is 40 to 50% homologous to members of the tyrosine kinase gene family. This tyrosine kinase domain is preceded by a hydrophobic sequence characteristic of a transmembrane domain. Transcription of the ret tyrosine kinase sequence was detected in the SK-N-SH neuroblastoma, HL-60 promyelocytic leukemia, and THP-1 monocytic leukemia cell lines, but not in 25 other human tumor cell lines surveyed. The ret tyrosine kinase may thus represent a cell surface receptor which is expressed in a restricted range of human cells.
Developmental regulation of SPO13, a gene required for separation of homologous chromosomes at meiosis I.
Authors: Wang H T , Frackman S , Kowalisyn J , Esposito R E , Elder R
Published: September 2015

Previous studies have demonstrated that the SPO13 gene is required for chromosome separation during meiosis I in Saccharomyces cerevisiae. In the presence of the spo13-1 nonsense mutation, MATa/MAT alpha diploid cells complete a number of events typical of meiosis I including premeiotic DNA synthesis, genetic recombination, and spindle formation. Disjunction of homologous chromosomes, however, fails to occur. Instead, cells proceed through a single meiosis II-like division and form two diploid spores. In this paper, we report the cloning of this essential meiotic gene and an analysis of its transcription during vegetative growth and sporulation. Disruptions of SPO13 in haploid and diploid cells show that it is dispensible for mitotic cell division. Diploids homozygous for the disruptions behave similarly to spo13-1 mutants; they sporulate at wild-type levels and produce two-spored asci. The DNA region complementing spo13-1 encodes two overlapping transcripts, which have the same 3' end but different 5' ends. The major transcript is 400 bases shorter than the larger, less abundant one. The shorter RNA is sufficient to complement the spo13-1 mutation. While both transcripts are undetectable or just barely detectable in vegetative cultures, they each undergo a greater than 70-fold induction early during sporulation, reaching a maximum level about the time of the first meiotic division. In synchronously sporulating populations, the transcripts nearly disappear before the completion of ascus formation. Nonsporulating cells homozygous for the mating-type locus show a small increase in abundance (less than 5% of the increase in sporulating cells) of both transcripts in sporulation medium. These results indicate that expression of the SPO13 gene is developmentally regulated and starvation alone, independent of the genotype at MAT, can trigger initial induction.
Differential expression of the ras gene family in mice.
Authors: Leon J , Guerrero I , Pellicer A
Published: September 2015

We compared the expression of the ras gene family (H-ras, K-ras, and N-ras) in adult mouse tissues and during development. We found substantial variations in expression among different organs and in the amounts of the different transcripts originating from each gene, especially for the N-ras gene. The expression patterns were consistent with the reported preferential tissue activation of ras genes and suggested different cellular functions for each of the ras genes.
The nontranscribed chicken calmodulin pseudogene cross-hybridizes with mRNA from the slow-muscle troponin C gene.
Authors: Putkey J A , Carroll S L , Means A R
Published: September 2015

A chicken calmodulin pseudogene with no introns was previously shown to hybridize under stringent conditions with an mRNA species present in skeletal and cardiac muscles, yet it would not hybridize to calmodulin mRNA (J. P. Stein, R. P. Munjaal, L. Lagace', E. C. Lai, B. W. O'Malley, and A. R. Means, Proc. Natl. Acad. Sci. USA 80:6485-6489, 1983). Using the pseudogene as a probe, we isolated a full-length cDNA corresponding to this mRNA from a chicken breast muscle library and showed by sequence analysis that it encodes slow-muscle troponin C and not the pseudogene product. Hybridization between the calmodulin pseudogene and slow-muscle troponin C cDNA is due to a short region of high homology in those nucleotides that encode helices B and C of troponin C and calmodulin. Genomic Southern analysis showed the calmodulin pseudogene and the gene for slow-muscle troponin C to exist as distinct single copies.
Factor interactions at simian virus 40 GC-box promoter elements in intact nuclei.
Authors: Buchanan R L , Gralla J D
Published: September 2015

Primer extension footprinting was used to probe late simian virus 40 regulatory elements in intact infected cell nuclei. Specific protection was observed over the viral "GC-box" transcription elements. The participation of the bound templates in gene activation is addressed by quantitation that shows that their abundance greatly exceeds that of transcription complexes but is comparable to that of open chromatin.
Cloning, sequence determination, and expression in transfected cells of the coding sequence for the tox 176 attenuated diphtheria toxin A chain.
Authors: Maxwell F , Maxwell I H , Glode L M
Published: September 2015

DNA including the coding sequence for the A chain of the mutant diphtheria toxin tox 176 was cloned. The cloned mature A-chain coding sequence showed a G-to-A transition at nucleotide 383 as the only difference from the wild-type sequence. This resulted in replacement of the glycine at position 128 by aspartic acid in the predicted amino acid sequence. A eucaryotic cell expression plasmid, pTH1-176, was constructed in which the tox 176 A-chain coding sequence was attached to a truncated metallothionein promoter. The toxicity of this construct, compared with that of the corresponding wild-type diphtheria toxin A-chain plasmid, pTH1, was assessed after transfection into the human 293 cell line by an indirect transient expression assay (I. H. Maxwell, F. Maxwell, and L. M. Glode, Cancer Res. 46:4660-4664, 1986). For the same effect, 15- to 30-fold more pTH1-176 than pTH1 was required, a result consistent with previous in vitro estimates of the diminished activity of the tox 176 A chain. Controlled expression of the cloned tox 176 A-chain coding sequence may provide a means of eliminating specific cell populations in an organism, for which purpose the wild-type diphtheria toxin A chain might prove too toxic.
Synthesis and localization of pathogenesis-related proteins in tobacco.
Authors: Carr J P , Dixon D C , Nikolau B J , Voelkerding K V , Klessig D F
Published: September 2015

The PR1 family of pathogenesis-related proteins from tobacco (Nicotiana tabacum L.) leaves is induced by a variety of pathogenic and chemical agents and is associated with resistance to tobacco mosaic virus. The majority of the PR1 proteins did not copurify with mesophyll protoplasts (the major cell type of the leaf) isolated from tobacco mosaic virus-infected N. tabacum cv. Xanthi-nc leaves. However, these isolated protoplasts were capable of synthesizing and selectively secreting the PR1 proteins. Using monoclonal antibodies for immunofluorescence microscopy, we localized these proteins to the extracellular spaces predominantly in regions adjacent to viral lesions as well as in xylem elements of infected leaves.
DNA sequence-directed nucleosome reconstitution on 5S RNA genes of Xenopus laevis.
Authors: Gottesfeld J M
Published: September 2015

Nucleosomes were reconstituted in vitro with several singly end-labeled restriction fragments derived from a cloned somatic-type 5S RNA gene of Xenopus laevis and purified nucleosome core particles from Xenopus cultured cells or chicken erythrocytes. Nucleosome locations were determined by digestion of the reconstitutes with exonuclease III and DNase I and were the same for all fragments investigated, extending from 20 base pairs (bp) within the 5S gene to 80 bp beyond the 3' end of the gene. Both core particles and crude nuclear extracts gave equivalent results, suggesting that no factors other than the core histones are responsible for recognition of DNA sequence during reconstitution. The histone octamer and the 5S gene-specific transcription factor TFIIIA both bind to the same region and face of 5S DNA, and nucleosome reconstitution on the 5S gene excluded binding of TFIIIA. The helical repeat of somatic-type 5S DNA in solution was measured by the band shift method and was 10.5 to 10.6 bp per turn over the region of the TFIIIA-binding site. The difference in helical repeat between DNA in solution and on the surface of the nucleosome (10.0-bp spacing between DNase I cutting sites) may explain the linking number paradox.
Neoplastic transformation by the human gene N-myc.
Authors: Small M B , Hay N , Schwab M , Bishop J M
Published: September 2015

Amplification and abundant expression of a gene known as N-myc are found frequently in advanced stages of human neuroblastoma and may play a role in the genesis of several malignant human tumors. Previous studies have shown that N-myc can cooperate with a mutant allele of the proto-oncogene c-Ha-ras to transform embryonic rat cells in culture. Here we show that N-myc can also act alone to elicit neoplastic growth of an established line of rat fibroblasts (Rat-1). We used recombinant DNA vectors to express either N-myc or its kindred gene c-myc in transfected cells. Both genes caused morphological transformation, anchorage-independent growth, and tumorigenicity. We noticed two variables that appeared to influence the ability to isolate cells transformed by N-myc and c-myc: the abundance in which the genes were expressed and biological selection to eliminate untransformed cells from the cultures. Our findings sustain the belief that N-myc is an authentic proto-oncogene, lend further credibility to the role of N-myc in the genesis of human tumors, and establish a convenient assay that can be used to explore further the properties of both N-myc and c-myc.
Both conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro.
Authors: Mowry K L , Steitz J A
Published: September 2015

Pre-mRNA substrates containing sequences from human and mouse histone genes are accurately processed in a HeLa cell nuclear extract to generate mature 3' termini. When in vitro processing reactions containing either human histone H3 or mouse histone H3 transcripts are treated with RNase T1 and probed with antibodies specific for the Sm protein determinants or for the trimethylguanosine cap structure unique to the U RNAs present in small nuclear ribonucleoproteins, RNA fragments that encompass the site of 3' end formation on the pre-mRNA transcript are selectively recovered. Several different interactions are detected: at time zero, the protected region contains the upstream conserved hairpin loop structure; at later times during the reaction, protection extends beyond the site of 3' end formation to include the downstream conserved sequence element and the 5' cap of the transcript is bound as well. Possible interactions between Sm small nuclear ribonucleoproteins and these conserved sequence elements in histone pre-mRNAs are discussed.
Characterization of nit-2, the major nitrogen regulatory gene of Neurospora crassa.
Authors: Fu Y H , Marzluf G A
Published: September 2015

The nit-2 gene is the major nitrogen-regulatory gene of Neurospora crassa, and under conditions of nitrogen limitations, it turns on the expression of various unlinked structural genes which specify nitrogen-catabolic enzymes. The nit-2 gene was subcloned as a 6-kilobase (kb) DNA fragment from a cosmid that carried approximately a 40-kb N. crassa DNA insert. The nit-2 gene was localized in a DNA segment of approximately 3.5 kb and was shown to correspond to a unique DNA sequence located on linkage group 1. Several N. crassa nit-2 transformants were characterized and were found to possess significantly different levels of the regulated enzyme nitrate reductase. Northern blot analysis of RNA from various strains was carried out to determine whether the nit-2 gene was expressed constitutively or was itself subject to regulation. The results revealed that the nit-2 gene is transcribed to give a single large mRNA of approximately 3.5 kb. Expression of the nit-2 gene is regulated such that its transcript is present at a substantially higher level in cells which are limited for nitrogen than in cells growing under nitrogen-repressed conditions. However, the nit-2 gene is not controlled by autogenous regulation. The nit-2 gene was transcribed only at a low level in nmr-1 and in gln-1b, under both nitrogen-repressed and derepressed conditions, suggesting that these unlinked loci may exert a positive regulatory effect on nit-2.
Developmental regulation of DNase I-hypersensitive sites in Dictyostelium discoideum.
Authors: Ayres K , Neuman W , Rowekamp W G , Chung S
Published: September 2015

We have studied two regions of Dictyostelium discoideum chromatin and identified several DNase I-hypersensitive sites in these regions. One of these sites is located about 300 to 500 bases upstream of the transcriptional start site of a gene that is expressed at all stages of development. This site is present in both vegetative cells and postaggregation cells. Another hypersensitive site is associated with a gene that is expressed only after the multicellular stage. This site is located about 400 bases upstream of the start site, and it is present only in postaggregation cells. Thus, much like higher eucaryotes, D. discoideum contains DNase I-hypersensitive sites that may be involved in the regulation of the genes with which they are associated.
Alterations in pp60c-src accompany differentiation of neurons from rat embryo striatum.
Authors: Cartwright C A , Simantov R , Kaplan P L , Hunter T , Eckhart W
Published: September 2015

Cultured neurons from rat embryo striatum were found to contain two structurally distinct forms of pp60c-src. The 60-kilodalton (kDa) form appeared similar to pp60c-src from cultured rat fibroblasts or astrocytes. The 61-kDa form was specific to neurons and differed in the NH2-terminal 18 kDa of the molecule. In undifferentiated neurons the predominant phosphorylated species of pp60c-src was the fibroblast form. Upon differentiation, a second phosphorylated form of pp60c-src was detected. This form had two or more additional sites of serine phosphorylation within the NH2-terminal 18-kDa region of the molecule, one of which was Ser-12. The specific protein-tyrosine kinase activity of the total pp60c-src population increased 14-fold, as measured by autophosphorylation, or 7-fold, as measured by phosphorylation of an exogenous substrate, as striatal neurons differentiated. This elevation in protein kinase activity occurred without a detectable decrease in Tyr-527 phosphorylation or increase in Tyr-416 phosphorylation. Our results support the idea that the expression of the neuron-specific form of pp60c-src and the increase in specific protein kinase activity may be important for neuronal differentiation.
Efficient association of in vitro translation products with purified stable Candida tropicalis peroxisomes.
Authors: Small G M , Imanaka T , Shio H , Lazarow P B
Published: September 2015

Newly synthesized peroxisomal proteins enter preexisting peroxisomes posttranslationally in vivo, generally without proteolytic processing. An efficient reconstitution of this process in vitro together with cloned DNAs for peroxisomal proteins would make possible investigation of the molecular information that targets proteins to peroxisomes. We have previously reported the isolation of clones for Candida tropicalis peroxisomal proteins; here we describe the association (and possible import) of peroxisomal proteins with peroxisomes in vitro. C. tropicalis was grown in a medium containing Brij 35, resulting in the induction of a moderate number of medium-sized peroxisomes. These peroxisomes, isolated in a sucrose gradient, had a catalase latency of 54% and were sufficiently stable to be concentrated and used in an import assay. The reticulocyte lysate translation products of total RNA from oleate-grown cells were incubated with the peroxisomes at 26 degrees C in the presence of 50 mM KCl, protease inhibitors, 0.5 M sucrose, 2.5 mM MOPS (morpholinepropanesulfonic acid) (pH 7.2), and 0.5 mM EDTA. Ten major translation products (which could be immunoprecipitated with antiserum against peroxisomal protein) became progressively associated with the peroxisomes during the first 30 min of incubation (some up to approximately 70%). These include acyl coenzyme A oxidase and the trifunctional protein hydratase-dehydrogenase-epimerase. This association did not occur at 4 degrees C nor did it occur if the peroxisomes were replaced with mitochondria.
Albumin and alpha-fetoprotein gene transcription in rat hepatoma cell lines is correlated with specific DNA hypomethylation and altered chromatin structure in the 5' region.
Authors: Tratner I , Nahon J L , Sala-Trepat J M , Venetianer A
Published: September 2015

We examined DNA methylation and DNase I hypersensitivity of the alpha-fetoprotein (AFP) and albumin gene region in hepatoma cell lines which showed drastic differences in the level of expression of these genes. We assayed for methylation of the CCGG sequences by using the restriction enzyme isoschizomers HpaII and MspI. We found two methylation sites located in the 5' region of the AFP gene and one in exon 1 of the albumin gene for which hypomethylation is correlated with gene expression. Another such site, located about 4,000 base pairs upstream from the AFP gene, seems to be correlated with the tissue specificity of the cells. DNase I-hypersensitive sites were mapped by using the indirect end-labeling technique with cloned genomic DNA probes. Three tissue-specific DNase I-hypersensitive sites were mapped in the 5' flanking region of the AFP gene when this gene was transcribed. Similarly, three tissue-specific DNase I-hypersensitive sites were detected upstream from the albumin gene in producing cell lines. In both cases, the most distal sites were maintained after cessation of gene activity and appear to be correlated with the potential expression of the gene. Interestingly, specific methylation sites are localized in the same DNA region as DNase I hypersensitive sites. This suggests that specific alterations of chromatin structure and changes in methylation pattern occur in specific critical regulatory regions upstream from the albumin and AFP genes in rat hepatoma cell lines.
Transcriptional regulation of an hsp70 heat shock gene in the yeast Saccharomyces cerevisiae.
Authors: Slater M R , Craig E A
Published: September 2015

The yeast Saccharomyces cerevisiae contains three heat-inducible hsp70 genes. We have characterized the promoter region of the hsp70 heat shock gene YG100, that also displays a basal level of expression. Deletion of the distal region of the promoter resulted in an 80% drop in the basal level of expression without affecting expression after heat shock. Progressive-deletion analysis suggested that sequences necessary for heat-inducible expression are more proximal, within 233 base pairs of the initiation region. The promoter region of YG100 contains multiple elements related to the Drosophila melanogaster heat shock element (HSE; CnnGAAnnT TCnnG). Deletion of a proximal promoter region containing one element, HSE2, eliminated most of the heat-inducible expression of YG100. The upstream activation site (UAS) of the yeast cytochrome c gene (CYC1) can be substituted by a single copy of HSE2 plus its adjoining nucleotides (UASHS). This hybrid promoter displayed a substantial level of expression before heat shock, and the level of expression was elevated eightfold by heat shock. YG100 sequences that flank UASHS inhibited basal expression of UASHS in the hybrid promoter but not its heat-inducible expression. This inhibition of basal UASHS activity suggests that negative regulation is involved in modulating expression of this yeast heat shock gene.
Expression of three genes for elongation factor 1 alpha during morphogenesis of Mucor racemosus.
Authors: Linz J E , Sypherd P S
Published: September 2015

Three genes, TEF-1, -2, and -3, encode elongation factor 1 alpha in Mucor racemosus. Neutral and alkaline S1 nuclease analyses revealed that the genetic organization is unique for each of the genes. The number and size of the intervening sequences vary in these closely related genes, which suggests that complex genetic rearrangements gave rise to the elongation factor 1 alpha gene family. Nucleotide sequence data from restriction fragments isolated from the 5' and 3' ends of TEF-2 and -3 confirmed the presence of a second intervening sequence in these genes. These data along with S1 nuclease mapping revealed a region at the 3' end of the three genes which was predicted to be transcribed but untranslated. Unique oligonucleotides containing 19 bases were synthesized to hybridize to this unique trailer region in the elongation factor 1 alpha transcripts. These oligonucleotides were used as probes in standard Northern analysis of RNA purified from M. racemosus cells of several morphological types. It was determined that all three genes were expressed in the cell morphological types studied. However, the accumulated level of transcript derived from each gene varied considerably, with TEF-1 mRNA present in approximately twofold greater quantity than the TEF-3 transcript and up to sixfold greater quantity than TEF-2. The level of TEF-1 and -2 mRNA varied little among the cell morphological types studied, whereas TEF-3 mRNA was present in twofold greater quantity in sporangiospores than in either germlings or yeast cells which had been induced to undergo morphogenesis to hyphae. These data suggest that there is differential expression of the genes encoding elongation factor 1 alpha in M. racemosus. At least one gene, TEF-3, shows a morphology-specific pattern of transcript accumulation.
Expression of six mouse major urinary protein genes in the mammary, parotid, sublingual, submaxillary, and lachrymal glands and in the liver.
Authors: Shahan K , Denaro M , Gilmartin M , Shi Y , Derman E
Published: September 2015

Mouse major urinary proteins (MUPs) are encoded by a family of about 35 to 40 highly conserved genes. In the preceding paper (K. Shahan, M. Gilmartin, and E. Derman, Mol. Cell. Biol. 7:1938-1946, 1987), we presented the sequences of the most abundant MUP mRNAs in the liver (MUP I, II, and III) and in the lachrymal (MUP IV) and submaxillary (MUP V) glands. We have shown that these five mRNAs are coded by five distinct genes, MUP I through V. In the present communication, we examine the expression of MUP genes in all of the six tissues in which MUP mRNAs are synthesized, the mammary, parotid, sublingual, lachrymal, and submaxillary glands and the liver. We show that gene MUP II is expressed in the liver and in the mammary gland, that gene MUP IV is expressed in the lachrymal and parotid glands, and that gene MUP V is expressed in the submaxillary, sublingual, and lachrymal and parotid glands, and that gene MUP V is expressed in the submaxillary, sublingual, and lachrymal glands. Furthermore, we present evidence that in addition to genes MUP I through V, another gene, MUP VI, is expressed in BALB/c mice in the parotid gland. The tissue-specific synthesis of MUP mRNAs is thus brought about by two major mechanisms: the expression, in different tissues, of different members of the family and the expression of a single gene at various levels in different tissues. When a particular MUP gene is expressed in several tissues, transcripts of this gene initiate at the same site and are spliced and polyadenylated in the same manner.