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PubMed1992

Regulation of Myc: Max complex formation and its potential role in cell proliferation.

The myc family of proto-oncogenes encodes short-lived nuclear phosphoproteins (Myc) involved in the control of cell proliferation and differentiation. Here we discuss the evidence for Myc's involvement in normal and abnormal cell proliferation and review recent information on Max, a novel protein that forms a sequence-specific DNA-binding complex with Myc. The properties of the Myc: Max heterodimeric complex suggest a model for how Myc may function in the cell.

Animals↗
PubMed2016

Toxin-Antitoxin Systems of Staphylococcus aureus.

Toxin-antitoxin (TA) systems are small genetic elements found in the majority of prokaryotes. They encode toxin proteins that interfere with vital cellular functions and are counteracted by antitoxins. Dependent on the chemical nature of the antitoxins (protein or RNA) and how they control the activity of the toxin, TA systems are currently divided into six different types. Genes comprising the TA types I, II and III have been identified in Staphylococcus aureus. MazF, the toxin of the mazEF locus is a sequence-specific RNase that cleaves a number of transcripts, including those encoding pathogenicity factors. Two yefM-yoeB paralogs represent two independent, but auto-regulated TA systems that give rise to ribosome-dependent RNases. In addition, omega/epsilon/zeta constitutes a tripartite TA system that supposedly plays a role in the stabilization of resistance factors. The SprA1/SprA1AS and SprF1/SprG1 systems are post-transcriptionally regulated by RNA antitoxins and encode small membrane damaging proteins. TA systems controlled by interaction between toxin protein and antitoxin RNA have been identified in S. aureus in silico, but not yet experimentally proven. A closer inspection of possible links between TA systems and S. aureus pathophysiology will reveal, if these genetic loci may represent druggable targets. The modification of a staphylococcal TA toxin to a cyclopeptide antibiotic highlights the potential of TA systems as rather untapped sources of drug discovery.

Antitoxins↗
PubMed2026

miR-197 Targets NLRP3 3' UTR and Correlates with NLRP3/Caspase-1/IL-18 Signaling in Hyperoxia-Stimulated Neonatal BPD Mouse Model.

Reduced circulating miR-197 was previously observed in preterm infants who later developed bronchopulmonary dysplasia (BPD), but its relationship with NLRP3 inflammasome signaling remains unclear. This study examined miR-197 expression, NLRP3 inflammasome-related markers, and the interaction between miR-197 and the NLRP3 3' UTR in a neonatal hyperoxia model. Neonatal C57BL/6J mice were exposed to 60% oxygen or room air from birth, and lung tissues were collected on postnatal days 1, 7, 14, and 21. Lung injury and alveolar development were assessed by histology, radial alveolar count, mean linear intercept, and lung wet-to-dry ratio. miR-197 and NLRP3 expression and NF-κB-, caspase-1-, and IL-18-related proteins were evaluated by RT-qPCR and Western blotting. A dual-luciferase reporter assay in MLE12 cells tested the interaction between miR-197 and the NLRP3 3' UTR. Hyperoxia increased lung wet-to-dry ratios and mean linear intercept, reduced radial alveolar count, and caused progressive alveolar simplification. miR-197 expression decreased, whereas NLRP3 mRNA increased, at all examined time points; NLRP3 protein and inflammasome-related protein changes were most evident from postnatal day 7 onward. The miR-197 mimic reduced luciferase activity in the wild-type but not mutant NLRP3 3' UTR reporter. These findings show that neonatal hyperoxia is associated with reduced miR-197 and increased NLRP3/inflammasome-related signaling and support a sequence-specific interaction between miR-197 and the NLRP3 3' UTR, although causal regulation in vivo requires further investigation.

Animals↗
PubMed1992

[Gene amplification with PCR and sequence specific HLA oligonucleotide typing].

Genetic polymorphism in the HLA class II region has been identified by the analysis of the polymerase chain reaction (PCR) products using sequence-specific oligonucleotide (SSO). The PCR-SSO method permits precise and direct analysis of allelic variations with as little as 1 microgram of genomic DNA. The standardized, uniform hybridization and critical wash protocol of the Eurotransplant typing kit enables HLA typing independent of gene expression and quality of lymphocytes. One of the advantages of this technique is that the definition of splits is much better than typing by serology.

Base Sequence↗
PubMed1992

Tachyplesin I as a model peptide for antiparallel beta-sheet DNA binding motif.

In this study, we present a model compound for antiparallel beta-sheet-DNA interaction. Tachyplesin I, cationic antimicrobial peptide, interacts through contacts with the minor groove. Secondary structure of tachyplesin I, antiparallel beta-sheet constrained by two disulfide bridges and connected by beta-turn, contributes significantly to its DNA binding. The present results give valuable information for design of sequence-specific DNA binding peptide based on antiparallel beta-sheet.

Amino Acid Sequence↗
PubMed1992

Interaction of a protooncogene product, Myb with DNAs.

The DNA-binding domain of Myb consists of three imperfect tandem repeats and the third one which is essential for sequence-specific binding was established to have a helix-turn-helix-related motif. DNA sequences recognized by Myb have been reported to contain TAACPy sequence. Here we have examined the details of Myb-binding sequence. Using DNAs with a single mutation on the various sites of two specific DNAs and some fragments of the DNA-binding domain of Myb, we have found that (i) in a specific DNA which contains only one AAC sequence, each AAC nucleotide is found to be essential for the specific binding of Myb, while any other mutations cause no serious binding loss, (ii) in a specific DNA which contains two AAC sequences separately, one AAC is not so important in the binding, and (iii) for the specific binding with DNA, at least both repeats 2 and 3 of Myb are required. These findings suggest that repeat 3 containing a helix-turn-helix-related structure recognizes the core AAC sequence and repeat 2 supports this recognition by interactions with phosphate groups of DNA.

Base Sequence↗
PubMed1992

Recognition of (d(TTTATT) and d(TTATTT) by capillary affinity gel electrophoresis (CAGE) using poly(9-vinyladenine)-polyacrylamide conjugated gel.

Sequence-specific recognition of oligodeoxynucleotide isomers (TTTATT and TTATTT) was achieved by using polyacrylamide-poly(9-vinyladenine) conjugated gel filled capillary affinity gel electrophoresis. It was found that the interaction between poly(9-vinyladenine) and the isomers was dependent on the sequential thymidylic acids of them.

Adenine↗
PubMed1992

Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins.

An automated method of running a tandem sequence of oligonucleotide affinity columns was used to purify factors that interact specifically with cis-regulatory sites of the CyIIIa cytoskeletal actin gene of the sea urchin embryo (Strongylocentrotus purpuratus). The method allows quantitative enrichment in a single chromatographic run of up to 12 different sequence-specific DNA binding proteins, each of which may then be readily purified to homogeneity by methods such as preparative gel electrophoresis. The affinity chromatography and identification of six different CyIIIa-regulatory factors is described, and the general utility of the method is discussed.

Actins↗
PubMed1992

Specific N-methylations of HPV-16 E7 peptides alter binding to the retinoblastoma suppressor protein.

Complex formation between the human papilloma virus type 16 E7 protein (HPV-16 E7) and the retinoblastoma growth suppressor protein (RB) is believed to contribute to the process of cellular transformation that leads to cervical carcinoma. Genetic analysis of the HPV-16 E7 protein has shown that the segment of E7 homologous to the conserved region 2 of adenovirus 5 E1A protein is involved in both RB binding and E7-mediated cell transformation. We have previously shown that a peptide colinear with HPV-16 E7 residues 21-29 was able to block immobilized species of E7 from binding to RB protein. The current study reports the effects of different chemical modifications of this peptide. One type of modification, methylation of the alpha-amino nitrogens contributed by Leu22, Tyr25, and Leu28, resulted in a 45-fold increase in E7/RB binding antagonist activity. This increased antagonist activity is sequence-specific since methylation of the amino groups contributed by Tyr23, Cys24, or Glu26 resulted in a profound loss of binding antagonist activity. Using a newly developed binding assay we determined that the apparent dissociation constant for recombinant HPV-16 E7 protein binding to recombinant human RB protein is 1.3 nM. The peptide Ac[N-MeLeu22,N-Me-Tyr25,N-MeLeu28]-(21-29)-E7 amide was determined to be a competitive inhibitor of HPV-16 E7 binding to RB with a Ki value of 32 nM.

Amino Acid Sequence↗
PubMed1992

DNA strand transfer reactions catalyzed by vaccinia topoisomerase I.

Vaccinia virus DNA topoisomerase I forms a 3'-phosphoryl intermediate with duplex DNAs containing the conserved binding/cleavage motif 5'CCCTT decreases. Covalently bound enzyme is capable of transferring the incised DNA strand to a heterologous DNA acceptor containing a 5'OH terminus. Both intramolecular and intermolecular religation reactions are catalyzed. Intramolecular strand transfer occurs to the noncleaved strand of the DNA duplex and results in formation of a hairpin loop. Intermolecular religation to an exogenous DNA strand is favored over hairpin formation and requires the potential for base pairing between the acceptor and the noncleaved strand of the donor complex. As few as 4 potential base pairs are sufficient to support intermolecular transfer. These results in vitro are consistent with the proposal that vaccinia topoisomerase can catalyze sequence-specific strand transfer during genetic recombination in vivo (Shuman, S. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 10104-10108.).

Autoradiography↗
PubMed1992

Cooperative interactions between replication origin-bound molecules of herpes simplex virus origin-binding protein are mediated via the amino terminus of the protein.

The virally encoded origin binding protein (OBP) of herpes simplex virus (HSV) is required for viral DNA synthesis. OBP binds at the replication origin to initimultienzyme replication complex (Challberg, M. D., and Kelly, T. J. (1989) Annu Rev. Biochem. 58, 671-717), OBP binds to two sites at the replication origin. The sequence-specific interaction of OBP with each binding site is localized to the major groove, and in both HSV origins the two interaction surfaces are in phase, aligned on the same face of the helix (Hazuda, D. J., Perry, H. C., Naylor, A. M., and McClements, W. L. (1991) J. Biol. Chem. 261, 24621-24625). Using native gel electrophoresis, we now demonstrate that OBP binding to the origin is highly cooperative and that cooperativity requires the putative NH2-terminal leucine zipper. Neither the phase nor orientation of the binding sites affect cooperativity, suggesting that the interaction promotes wrapping of origin DNA around the OBP multimer. A comparison of OBP DNase I footprints with the DNase I footprints of a truncated protein defective in cooperativity demonstrates that the interaction between OBPs bound at sites I and II affects the conformation of the intervening DNA, particularly when the phase or orientation of the two sites is different from wild type. OBP may elicit a unique nucleoprotein structure which facilitates unwinding of the origin and/or assembly of the replication complex. We also demonstrate that OBP can exchange binding sites, forming interduplex complexes. This property may be important for reinitiation of DNA replication.

Base Sequence↗
PubMed1992

The liver-enriched transcription factor D-site-binding protein activates the promoter of the phosphoenolpyruvate carboxykinase gene in hepatoma cells.

It has been previously demonstrated that the CCAAT/enhancer-binding protein (C/EBP) trans-activates the gene coding for the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) (PEPCK) and binds to several sites along the promoter. The additional observations that C/EBP is expressed in liver and follows the same developmental profile as PEPCK suggests that C/EBP plays an important role in the regulation of PEPCK gene expression. However, since C/EBP is expressed at high levels in lung, a tissue in which PEPCK is not expressed, it appears that other mechanisms are involved to provide PEPCK with high level expression in liver. We now show that the albumin promoter D-site-binding protein (DBP), a transcription factor whose expression is limited to the liver, is also able to trans-activate the PEPCK promoter through sequence-specific binding. Both recombinant DBP and C/EBP bind with highest affinity to regions located at positions -85 and -245 in the promoter, but display differences in their binding properties at other sites. Using eukaryotic expression vectors for both C/EBP and DBP, we found that with 5'-deletion mutants of the PEPCK promoter, both C/EBP and DBP exerted their effects through similar regions of the promoter. However, the use of internal deletion mutants of the promoter identified distinct differences in the mechanism of activation by C/EBP and DBP. In particular, a region of the promoter between positions -86 and -117 significantly attenuated the level of trans-activation by DBP, but not by C/EBP. Evidence presented also supports a model whereby the relative ratios of C/EBP and DBP in the cell fine-tune the expression of the PEPCK gene. These results demonstrate that DBP and C/EBP, while having similar DNA binding specificities, have distinct functional differences in the context of the PEPCK promoter. These differences, along with the developmental profiles of C/EBP and DBP, may provide a mechanistic explanation for the liver-specific as well as the developmental profile of PEPCK gene expression.

Binding Sites↗
PubMed1992

Localization of the single-stranded DNA binding site in the thrombin anion-binding exosite.

Single-stranded DNA molecules containing a 15-nucleotide consensus sequence have been reported to inhibit thrombin activity. The mechanism of the inhibition was studied using a consensus 15-mer oligonucleotide and two recombinant mutant thrombins: the anion-binding exosite mutant thrombin R70E, and thrombin K154A, in which the mutation was located in a surface loop outside of the exosite. The consensus 15-mer oligonucleotide inhibited both fibrinogen-clotting and platelet-activation activities of plasma-derived thrombin, recombinant wild type thrombin, and mutant thrombin K154A in a sequence-specific and dose-dependent manner, whereas it did not inhibit either activity of mutant thrombin R70E. The 15-mer oligonucleotide also inhibited thrombomodulin-dependent protein C activation by plasma-derived thrombin. In competition equilibrium binding experiments, binding of 125I-labeled diisopropyl phosphoryl-thrombin to thrombomodulin was completely inhibited by the consensus 15-mer oligonucleotide with a Kd value of 2.68 +/- 0.16 nM. These results suggest that Arg-70 in the anion-binding exosite of thrombin is a key determinant for interaction with specific single-stranded DNA molecules, and that binding of single-stranded DNA molecules to the exosite prevents the interaction of thrombin with fibrinogen, the platelet thrombin receptor, and thrombomodulin.

Base Sequence↗
PubMed1992

Purification and characterization of a transcription factor which appears to regulate cAMP responsiveness of the human CYP21B gene.

A unique cAMP regulatory sequence, -129/-96 base pairs (bp), associated with the gene encoding human cytochrome P450C21 (CYP21B) binds a nuclear protein designated ASP, as described previously (Kagawa, N., and Waterman, M. R. (1991) J. Biol. Chem. 266, 11199-11204). This putative transcription factor required for cAMP-dependent transcription of the human CYP21B gene has been purified from the nuclear extracts of mouse Y1 cells by using sequence-specific DNA-affinity chromatography. The purified ASP is 78 kDa as estimated by SDS-polyacrylamide gel electrophoresis and binds to its specific recognition site, -126/-113-bp CACTCTGTGGGCGG, which has been demonstrated to be the minimum cAMP regulatory sequence of the human CYP21B gene. To characterize ASP more precisely, an antibody was raised against the 78-kDa protein. This antibody led to a supershift of the DNA.ASP complex on gel shift analysis and inhibition of in vitro transcription promoted by the ASP binding sequence, thereby indicating that ASP is a 78-kDa transcription factor. Upon DNase I footprinting experiments, ASP showed a characteristic footprint which very closely resembles but is distinct from that of Sp1 which also occupies a binding site within -129/-96 bp. Furthermore, the addition of purified ASP enhanced the mRNA synthesis promoted by the minimum cAMP regulatory sequence in a cell-free transcription system using HeLa cell extracts, whereas added Sp1 does not. These results indicate that ASP is a primary transcription factor for the cAMP-dependent regulation of the human CYP21B gene.

Animals↗
PubMed1992

Identification of cis- and trans-acting factors regulating the expression of rat salivary-specific RP4 gene.

The molecular basis of tissue-specific and cyclic AMP (cAMP)-inducible gene expression in salivary glands is not well understood. Previously, we cloned a salivary-specific proline-rich protein gene, RP4. To analyze the cis-regulatory element(s) that mediates the regulation of this rat salivary RP4 gene, chimeric pRP4CAT constructs containing up to 1.7 kb of the 5'-flanking region of RP4 fused to a reporter gene were transiently transfected into salivary cells. Deletion studies suggest that a 159 bp (-147/+12) fragment of the RP4 5'-flanking region is sufficient to confer salivary-specific induction by agents that can raise intracellular cAMP concentration. Further delineation of this essential sequence revealed that a segment from -136 to -109 is necessary and sufficient to confer cAMP responsiveness in a salivary-specific manner when linked to a heterologous promoter. However, this 28 bp fragment (-136/-109) does not contain an identical match to the consensus cAMP response element (CRE). DNA mobility shift binding assays establish that a sequence-specific DNA-protein complex is formed between this DNA fragment and nuclear proteins from salivary cells, but not with nuclear proteins from HeLa cells, which contain canonical CRE binding proteins (CREBs). Taken together, these data demonstrate that we have identified a 28 bp cis-regulatory element in the RP4 gene that mediates salivary-specific cAMP-inducible gene expression. We propose that the novel salivary-specific CRE binding protein (SCBP) is a key regulator for salivary cAMP-inducible gene expression.

Animals↗
PubMed1992

[Relationship between drug resistance and oncogenes in lung cancer cell lines].

The 5-year survival of lung cancer patients is about 30% in Japan. One of the reasons for the poor prognosis seems to be drug resistance. It has been reported that certain types of oncogenes, such as ras, myc and fos, may play an important role in drug resistance. The myc protein forms a sequence-specific DNA-binding complex with Max and may act as a transcription factor; thus, it may be possible that myc family oncogenes are involved in DNA synthesis and repair processes mediating drug resistance. We report here that L-myc oncogene may be involved in the transition from drug-sensitive to drug-resistant phenotype of a certain small cell lung cancer cell line.

Animals↗
PubMed1992

Activation of muscle-specific transcription by myogenic helix-loop-helix proteins.

Myogenin is a muscle-specific transcription factor that acts as a molecular switch to induce myogenesis. Myogenin shares homology with MyoD and other myogenic regulatory proteins within a basic region and helix-loop-helix (HLH) motif that mediate binding to a conserved DNA sequence (CANNTG) present in the regulatory regions of numerous muscle-specific genes. Binding of myogenin and other members of the MyoD family to DNA can be augmented upon heterodimerization with the widely expressed HLH protein E12. We have used the muscle creatine kinase (MCK) enhancer as a target to study the mechanism whereby myogenin activates muscle-specific transcription. Full activity of the MCK enhancer requires cooperative interactions between myogenin (or other myogenic HLH proteins that bind the same site) and a complex array of ubiquitous and cell type-specific nuclear factors. To define the domains of myogenin responsible for sequence-specific DNA binding, activation of muscle-specific transcription, and cooperativity with other transcription factors, we have generated an extensive series of mutants by site-directed mutagenesis and domain swapping. These mutants have revealed strong transcriptional activation domains in the N- and C-termini of myogenin that rely on a specific amino acid sequence within the DNA binding domain for activity. Myogenin's ability to induce muscle-specific transcription is subject to negative regulation by growth factor and oncogenic signals. Mechanisms through which growth signals may repress myogenin function are discussed.

Animals↗
PubMed1992

Common sequence motifs at the rearrangement sites of a constitutional X/autosome translocation and associated deletion.

Reciprocal chromosome translocations are common de novo rearrangements that occur randomly throughout the human genome. To learn about causative mechanisms, we have cloned and sequenced the breakpoints of a cytologically balanced constitutional reciprocal translocation, t(X;4)(p21.2;q31.22), present in a girl with Duchenne muscular dystrophy (DMD). Physical mapping of the derivative chromosomes, after their separation in somatic cell hybrids, reveals that the translocation disrupts the DMD gene in Xp21 within the 18-kb intron 16. Restriction mapping and sequencing of clones that span both translocation breakpoints as well as the corresponding normal regions indicate the loss of approximately 5 kb in the formation of the derivative X chromosome, with 4-6 bp deleted from chromosome 4. RFLP and Southern analyses indicate that the de novo translocation is a paternal origin and that the father's X chromosome contains the DNA that is deleted in the derivative X. Most likely, deletion and translation arose simultaneously from a complex rearrangement event that involves three chromosomal breakpoints. Short regions of sequence homology were present at the three sites. A 5-bp sequence, GGAAT, found exactly at the translocation breakpoints on both normal chromosomes X and 4, has been preserved only on the der(4) chromosome. It is likely that the X-derived sequence GGAATCA has been lost in the formation of the der(X) chromosome, as it matches an inverted GAATCA sequence present on the opposite strand exactly at the other end of the deleted 5-kb fragment. These findings suggest a possible mechanism which may have juxtaposed the three sites and mediated sequence-specific breakage and recombination between nonhomologous chromosomes in male meiosis.

Base Sequence↗