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At least 1,153 records · Page 64Linked to original sources

PubMed1994

Region of insect high mobility group (HMG) 1 protein homologous to helix 2 of the rat HMG1-b box is in close contact with DNA.

The dipteran insects Chironomus and Drosophila have high mobility group (HMG) 1 proteins that are similar to mammalian HMG1 but contain one instead of two HMG1 boxes. The interaction of the Chironomus HMG1 proteins cHMG1a and cHMG1b with double-stranded and four-way junction DNA was analyzed by investigating the accessibility of defined sequences of the HMG1 box to specific antibodies within the DNA-protein complex in vitro. Antibody epitopes located in the three helices and in the turn between helices 1 and 2 of the HMG1 box were identified on a membrane onto which 90 decapeptides with overlapping sequences spanning the entire sequence of cHMG1a had been bound. Monospecific antibodies directed against selected epitopes were purified from a polyclonal antiserum by affinity chromatography. Helices 1 and 3 as well as the turn between helices 1 and 2 were found to be accessible to antibodies in the complex. In contrast, antibodies recognizing an epitope on putative helix 2 of cHMG1a and cHMG1b were unable to produce supershifts on gels of the DNA-protein complexes with both DNAs. These data suggest that helix 2 of the HMG1 box of proteins cHMG1a and cHMG1b is essentially responsible for contacts with DNA.

Amino Acid Sequence↗

PubMed1993

A Y-box consensus sequence is required for basal expression of the human multidrug resistance (mdr1) gene.

Basal transcription of the human multidrug resistance (mdr1) promoter was studied by chloramphenicol acetyltransferase (CAT) reporter fusion gene analysis in two parental and doxorubicin-resistant human tumor cell lines. Deletion of mdr1 DNA sequences to -89 relative to the start of transcription (at +1) had little effect on expression. Deletion of nucleotide sequences from -89 to -70, however, resulted in a 5-10-fold reduction in mdrCAT expression. DNase I footprint analysis demonstrated that the region from -85 to -70 was protected from nuclease digestion using nuclear extracts from these cell lines. The sequence between -82 and -73 is perfectly homologous with the 10-base pair Y-box consensus sequence found in the promoters of all major histocompatibility complex class-II (MHC II) genes. The Y-box sequence in MHC II genes is required for accurate and efficient transcription and contains the sequence CCAAT in the reverse orientation (Dorn, A., Durand, B., Marfing, C., Le Meur, M., Benoist, C., and Mathis, D. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 6249-6253). Mutations in the reverse CCAAT sequence of the Y-box consensus substantially reduced expression of an mdrCAT vector and eliminated nucleoprotein binding in an electrophoretic mobility shift assay. These results suggest that proteins which bind to the putative Y-box consensus sequence are critical for basal transcriptional regulation of the human mdr1 gene.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1994

High affinity interaction of dipteran high mobility group (HMG) proteins 1 with DNA is modulated by COOH-terminal regions flanking the HMG box domain.

The cells of the dipteran insects Chironomus and Drosophila contain high mobility group (HMG) 1 proteins that are homologous to the HMG1 protein of mammals but comprise one instead of two DNA-binding HMG boxes. Mobility shift assays have revealed that Chironomus cHMG1a and cHMG1b bind double strand and four-way junction DNA in a similar way at apparent dissociation constants in the range of 7.5-20 x 10(-9) M. Both proteins are monomeric and highly asymmetric molecules in solution. cHMG1a and cHMG1b exhibit Stokes' radii of 2.4 and 2.3 nm, respectively, and both show a frictional ratio of 1.5. Despite these similarities in their hydrodynamic properties, the binding site of cHMG1a on DNA is approximately 1.5 of the size found for the cHMG1b. Enzymatically and chemically prepared peptides of cHMG1a as well as bacterially expressed cHMG1a with terminal deletions and point substitutions showed that sequences flanking the folded domain that constitutes the HMG box are essential for the interaction of the HMG box with DNA. In particular, changes in the number of positive and negative charges, respectively, within basic and acidic domains modulated the DNA binding affinity of the cHMG1a protein. The alteration of fluorescence of the Trp residues suggest that this modulation is due to interaction of the acidic domain with the positively charged HMG box.

Amino Acid Sequence↗

PubMed1993

HMG box proteins in early T-cell differentiation.

The central theme of this review is the molecular basis for commitment of cells to the T-cell lineage. Principles of transcriptional regulation are illustrated by two examples; the role of GATA-1 during erythroid differentiation and the function of MyoD-like proteins in myogenesis. Several regulatory proteins have been described in the T-cell lineage. Here, we focus attention on the HMG box family of DNA binding proteins. This recently defined family can be divided in two subfamilies: the HMG/UBF and the TCF/SOX group. The first group contains at least two HMG boxes and binds DNA non-specifically, while the other group of proteins has one HMG box and interacts with DNA sequence-specifically. Characteristics of the most prominent members of both subfamilies will be discussed. In particular, we will address the role of HMG box proteins in controlling the expression of T-cell specific proteins during differentiation.

Amino Acid Sequence↗

PubMed1993

[Toxocara ova in parks and sand-boxes in the city of Utrecht].

An investigation was carried out for the presence of Toxocara spp. eggs in public parks and children's sand-boxes in the city of Utrecht. The pollution of parks with the eggs of the dog's ascarid Toxocara canis is comparable with reports from other European cities. The eggs of Toxocara cati were found in small numbers only. Interestingly there was no difference between parks with or without formal exclusion of dogs. Most sand-boxes are polluted with the eggs of the ascarid of cats T. cati. Incidentally eggs of T. canis were found. Sand-boxes which were obviously kept clean or could be closed contained lower numbers of eggs. As children playing in sand-boxes have far more chances to contaminate themselves with Toxocara eggs than when playing in parks or on playgrounds, the question arises if not T. cati eggs constitute a greater menace, at least in urban areas, to public health than T. canis eggs.

Animals↗

PubMed1993

v-Src activates the expression of 92-kDa type IV collagenase gene through the AP-1 site and the GT box homologous to retinoblastoma control elements. A mechanism regulating gene expression independent of that by inflammatory cytokines.

The 92-kDa type IV collagenase (matrix metalloproteinase-9; MMP-9) is frequently expressed in cells showing an invasive nature during physiological and pathological processes, and the expression is strictly controlled by a variety of trans-membrane signals. Binding sites for NF-kB, Sp-1, and AP-1 are reportedly required for induction of MMP-9 gene expression by tumor necrosis factor-alpha or 12-O-tetradecanoylphorbol-13-acetate. Comparison of the sequence of the newly cloned mouse MMP-9 promoter region with our previous human isolate revealed that, in addition to the above mentioned elements, four units of GGGG(T/A)GGGG sequence (GT box) were conserved between the two species. In this study, we have demonstrated that one of the GT boxes located downstream of the AP-1 site is essential along with the AP-1 site for the activation of the promoter by v-Src but not by tumor necrosis factor-alpha or 12-O-tetradecanoylphorbol-13-acetate. Gel mobility-shift assays revealed that binding proteins for retinoblastoma control element, including Sp-1 family protein, can bind specifically to GT boxes. Thus, the v-Src signals to the AP-1 site and to the GT box homologous to retinoblastoma control element acted synergistically in transcriptional activation. These results suggest that certain v-Src-mediated signals are propagated along pathways that are independent of inflammatory cytokines.

Animals↗

PubMed1993

Functional analysis of the P box, a domain in cyclin B required for the activation of Cdc25.

Cyclin B-cdc2 complexes are kept inactive by inhibitory phosphorylations on Thr-14 and Tyr-15 of cdc2 until they are dephosphorylated at the end of G2 by the phosphatase cdc25. Recent work has suggested that a small region of cyclin B, which we call the P box, may contribute part of a phosphatase-activating domain to cdc25. Individual conservative substitutions at three invariant residues within the P box yield mutant cyclin B proteins that bind cdc2 in vitro and then show the predicted cell cycle arrest, with cdc25 remaining in the low activity interphase form and cyclin B-cdc2 complexes remaining phosphorylated and inactive. While the low activity interphase form of cdc25 cannot act on cdc2 complexed with a mutant P box cyclin, the high activity M phase form of cdc25 can. These results demonstrate that the P box domain of cyclin B is required for cdc25 activation and support a two-step mechanism for the cdc25-dependent activation of cyclin B-cdc2.

Amino Acid Sequence↗

PubMedDate not supplied

Two-year results with box-only resin composite restorations.

One of the restorative alternatives in the treatment of proximal carious lesions is the box-only approach. This paper describes baseline and two-year results with 68 box-only resin composite restorations in a clinical study. The restorations were made using a glass ionomer cement as a dentin replacement and a bevelled outline. In terms of treatment time (32 minutes) and postoperative sensitivity (4 cases), the box-only restorations show favorable properties in comparison to conventional Class II resin composite restorations. At the two-year assessment no failures were observed, with fair results regarding clinical characteristics. It is concluded that, although applied to a limited number of teeth, the results indicate that the box-only approach with resin composites may make a contribution to the tooth-tissue-saving, restorative techniques.

Adult↗

PubMedDate not supplied

Clinical experience with an anatomic snuff box arteriovenous fistula in hemodialysis patients.

The present study was performed to evaluate the clinical usefulness of an anatomical snuff box arteriovenous fistula with special reference to its short-term and long-term patency in 139 hemodialysis patients. A snuff box fistula was established in 139 patients, including 39 with diabetic nephropathy (DN group) and 100 with non diabetic nephropathy (non DN Group). Fistula blood flow was measured by Doppler ultrasound in 18 patients. Early and late obstruction was observed in 24 (17%) of the 139 patients. The long-term patency rate of the snuff box fistula in the non DN group was 87% at 57 months, whereas the patency rate at 57 months in the DN group (72%) was significantly (p < 0.05) lower than that in the non DN group. The increase in arterialized vein blood flow in DN patients was less marked than that in the non DN patients. These results suggest that the high prevalence of late obstruction in DN patients may partly be reflected by an insufficient increase of arterialized vein blood flow at the snuff box site.

Adolescent↗

PubMed1996

The inhibition of cyclin B1 gene transcription in quiescent NIH3T3 cells is mediated by an E-box.

Cyclin Bl plays an important role in cell proliferation. Its expression is tightly regulated at the mRNA and protein levels during the cell cycle and is found to be deregulated in various malignancies. To enlighten the signalling pathways which lead to the cell cycle dependent expression of the cyclin B1 gene, we studied its transcriptional regulation in quiescent and proliferating NIH3T3 cells. We previously showed that the transcriptional activity of the cyclin B1 promoter decreases in quiescent cells. Here, we map a quiescence-responsive element of the human cyclin B1 promoter to an E-box sequence, CACGTG, which spans positions -124/-119. Nuclear proteins protect this sequence in a DNase I digestion assay and bind, in electromobility shift assays, an oligonucleotide spanning positions -133/-110. Max-specific antibodies block the DNA-binding activity of protein complexes to this probe. A mutation in the E-box core sequence abolishes the decrease in transcription that occurs during quiescence. Finally, we find that over-expression of Max protein in proliferating cells specifically inhibits cyclin B1 promoter activity through this E-box. Moreover, Max over-expression in proliferating NIH3T3 cells leads to down-regulation of the endogenous cyclin B1 protein. In conclusion, these data support a model whereby E-box-binding proteins mediate the decrease in the transcriptional activity of the cyclin B1 promoter observed in quiescent cells and suggest that Max contributes to this response.

3T3 Cells↗

PubMed1997

Efficient Cloning of Ascomycete Mating Type Genes by PCR Amplification of the Conserved MAT HMG Box

Cloning of mating type (MAT) genes from ascomycetes has been hampered by low conservation among them. One of the pair of MAT genes, represented by MAT-2 of Cochliobolus heterostrophus (a loculoascomycete) and mt a of Neurospora crassa (a pyrenomycete), encodes a protein with a conserved DNA binding motif called the high mobility group (HMG) box. PCR with primer pairs corresponding to the borders of the C. heterostrophus and the N. crassa HMG boxes generated an approximately 0.3-kb product from genomic DNAs of MAT-2 and mt a strains, respectively, but not from MAT-1 and mt A strains. The C. heterostrophus primers amplified approximately 0.3-kb products from DNA of most loculoascomycete genera tested but not from DNA of pyrenomycete genera; this specificity was reversed with the N. crassa primers. The validity of the PCR procedure was documented by near sequence identity between the C. heterostrophus MAT-2 HMG box and PCR products from several Cochliobolus spp. and by cosegregation of the PCR product with mating type in progeny of Setosphaeria turcica and of Cryphonectria parasitica. Regions of the MAT locus flanking the HMG box were readily cloned using the TAIL-PCR procedure with a combination of random and specific primers.

Journal Article↗

PubMed1997

Efficient cloning of ascomycete mating type genes by PCR amplification of the conserved MAT HMG Box.

Amino Acid Sequence↗

PubMed1997

Restoration of the CCAAT box or insertion of the CACCC motif activates [corrected] delta-globin gene expression.

Hemoglobin A2 (HbA2), which contains delta-globin as its non-alpha-globin, represents a minor fraction of the Hb found in normal adults. It has been shown recently that HbA2 is as potent as HbF in inhibiting intracellular deoxy-HbS polymerization, and its expression is therefore relevant to sickle cell disease treatment strategies. To elucidate the mechanisms responsible for the low-level expression of the delta-globin gene in adult erythroid cells, we first compared promoter sequences and found that the delta-globin gene differs from the beta-globin gene in the absence of an erythroid Krüppel-like factor (EKLF) binding site, the alteration of the CCAAT box to CCAAC, and the presence of a GATA-1 binding site. Second, serial deletions of the human delta-globin promoter sequence fused to a luciferase (LUC) reporter gene were transfected into K562 cells. We identified both positive and negative regulatory regions in the 5' flanking sequence. Furthermore, a plasmid containing a single base pair (bp) mutation in the CCAAC box of the delta promoter, restoring the CCAAT box, caused a 5.6-fold and 2.4-fold (P < .05) increase of LUC activity in transfected K562 cells and MEL cells, respectively, in comparison to the wild-type delta promoter. A set of substitutions that create an EKLF binding site centered at -85 bp increased the expression by 26.8-fold and 6.5-fold (P < .05) in K562 and MEL cells, respectively. These results clearly demonstrate that the restoration of either an EKLF binding site or the CCAAT box can increase delta-globin gene expression, with potential future clinical benefit.

Adult↗

PubMedDate not supplied

[A foldable cardboard box for drying and storage of by cotton swab collected biological samples].

The ability to perform successful DNA analysis on biological evidence obtained at a crime scene or during a sexual assault examination depends very much on the first step--how specimens are collected and preserved. Body fluids and their wet or dry stains, are often recovered using dry cotton swabs or cotton swabs moistened with sterile water or saline. In order to prevent decomposition and deterioration of a specimen, resulting in degradation or loss of DNA, it is recommended to either air dry or freeze these swabs as soon as possible after collection. We designed a simple, foldable cardboard box, which is suitable for the drying and storage of biological evidence collected on cotton swabs. Immediately after collection swabs are placed into the drying racks within the cardboard box, which is subsequently folded, labeled, sealed and initialed. At room temperature swabs completely air dry within the sealed box within 6-9 hours. In this box the evidence is properly packed, labelled and sealed, thus preventing cross contamination, degradation and sample switch. It is a valuable device for the collection of biological evidence at a crime scene, during sexual assault examinations, and for the collection of buccal swabs for PCR-based databasing and paternity testing.

DNA↗

PubMed1998

DNA bending by the chromosomal protein HMG1 and its high mobility group box domains. Effect of flanking sequences.

HMG1 is an evolutionarily highly conserved chromosomal protein consisting of two folded DNA-binding domains, A and B ("high mobility group (HMG) boxes"), and an acidic C-terminal domain. Several lines of evidence suggest that previously reported sequence-independent DNA bending and looping by HMG1 and its HMG box domains might be important for the proposed role of the protein in transcription and recombination. We have used ligase-mediated circularization assays to investigate the contribution of the individual A and B HMG1 box domains and of the linker region between A/B- and B/C-domains, which flank the "minimal" B-domain (residues 92-162), to the ability of the HMG1 protein (residues 1-215) to bend DNA. Neither the minimal B-domain nor the minimal B-domain with a 7-residue N-terminal extension (85TKKKFKD91) bent the DNA. The attachment of an extra 18-residue C-terminal additional extension (residues 163-180) to the minimal B-domain had only a small effect on the ability of the HMG box to bend DNA. On the other hand, circularization assay with a B-domain having both 7-residue N-terminal and 18-residue C-terminal flanking sequences (residues 85-180) revealed a strong bending of the DNA, suggesting that both extensions are a prerequisite for efficient DNA bending by the B-domain. We have also shown that a single lysine residue (Lys90) in a short N-terminal sequence 90KD91 attached to the B-domain is sufficient for strong distortion of DNA by bending, provided that the B-domain is flanked by the 18-residue C-terminal flanking sequence. Although the DNA bending potential of HMG1 seems to be predominantly due to the B-domain flanked by basic sequences, covalent attachment of the A- and B-domains is necessary for efficient DNA flexure and the ability of the (A+B)-bidomain to bend DNA is further modulated in the native HMG1 protein by its acidic C-domain.

Amino Acid Sequence↗

PubMed1998

Characterization of two distinct families of transcription factors that bind to the CCAAT box region of the human COL1A2 gene.

Both the mouse and human alpha2(I) procollagen promoters contain an inverted CCAAT box at -80, but only the human promoter contains an additional regulatory element, the collagen modulating element (CME), immediately downstream of the CCAAT box [Collins et al. (1997): Biochem J 322:199-206]. In this study, the transcription factors that bind to the G/CBE and CME within the human promoter were characterized in SVWI-38 and CT-1 nuclear extracts. Two distinct proteins bind to the CME, and both were identified as heat-labile factors that were sensitive to high ionic strengths and required Zn2+ for DNA-binding activity. These proteins had Stokes radii of 4.12 and 3.15 nm, sedimentation coefficients of 3.9 and 3.2 S and native molecular weights of 66 and 41 kDa, respectively. On the basis of biochemical and DNA-binding properties, the CME binding proteins are probably novel factors involved in the regulation of the human alpha2(I) procollagen gene. By contrast, the G/CBE binding proteins were more resistant to heat, ionic strength, and divalent metal ion chelators, demonstrating that the G/CBE and CME binding proteins had distinct DNA-binding properties. The above properties suggest that this factor is a member of the previously characterized family of CCAAT box-binding factors, CBF, NF-Y, CP-1 and alpha-CP1. Taken together, these physicochemical properties of the COL1A2 CCAAT box and CME-binding proteins demonstrated that they were distinct unrelated transcription factors. These results also suggest that there is a distinct difference in the DNA-binding activity between the equivalent region of the mouse and human alpha2(I) procollagen promoters.

Animals↗

PubMed1996

How proteins recognize the TATA box.

The crystal structure of a complex of human TATA-binding protein with TATA-sequence DNA has been solved, complementing earlier TBP/DNA analyses from Saccharomyces cerevisiae and Arabidopsis thaliana. Special insight into TATA box specificity is provided by considering the TBP/DNA complex, not as a protein molecule with bound DNA, but as a DNA duplex with a particularly large minor groove ligand. This point of view provides explanations for: (1) why T.A base-pairs are required rather than C.G; (2) why an alternation of T and A bases is needed; (3) how TBP recognizes the upstream and downstream ends of the TATA box in order to bind properly; and (4) why the second half of the TATA box can be more variable than the first.

Amino Acid Sequence↗

PubMed1998

Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II.

We have examined the role of the TATA box in determining transcription initiation frequency in vitro by studying a collection of promoters containing different TATA sequences in the context of the adenovirus major late promoter. In addition to measuring transcription rates, we have determined how the sequence changes affected the association and dissociation kinetics and the affinity of TBP binding. We observed that transcription from promoters containing the highest affinity TATA boxes is limited by the rate with which TBP associates with the promoter. In contrast, transcription from promoters containing lower affinity TATA boxes appears to be limited both by how much TBP is bound and by the relatively low occupancy of the conformation that can undergo subsequent steps in preinitiation complex assembly. The implications of these results in understanding the mechanism of transcription enhancement by transcriptional activators is discussed.

Adenoviridae↗