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At least 1,261 records · Page 70Linked to original sources
PubMed2002

A novel role of Sp1 and Sp3 in the interferon-gamma -mediated suppression of macrophage lipoprotein lipase gene transcription.

The regulation of macrophage lipoprotein lipase by cytokines is of potentially crucial importance in the pathogenesis of atherosclerosis. We have shown previously that macrophage lipoprotein lipase expression is suppressed by interferon-gamma (IFN-gamma) at the transcriptional level. We investigated the regulatory sequence elements and the transcription factors that are involved in this response. We demonstrated that the -31/+187 sequence contains the minimal IFN-gamma-responsive elements. Electrophoretic mobility shift assays showed that the binding of proteins to two regions in the -31/+187 sequence was reduced dramatically when the cells were exposed to IFN-gamma. Both competition electrophoretic mobility shift assays and antibody supershift assays showed that the interacting proteins were composed of Sp1 and Sp3. Mutations of the Sp1/Sp3-binding sites in the minimal IFN-gamma-responsive elements abolished the IFN-gamma-mediated suppression of promoter activity, whereas multimers of the sequence were able to impart the response to a heterologous promoter. Western blot analysis showed that IFN-gamma reduced the steady state levels of Sp3 protein. In contrast, the cytokine decreased the DNA binding activity of Sp1 without affecting the protein levels. These studies therefore reveal a novel mechanism for IFN-gamma-mediated regulation of macrophage gene transcription.

Base Sequence↗
PubMed1997

Modern thoughts on an ancyent marinere: function, evolution, regulation.

The mariner/Tc1 superfamily of transposable elements is one of the most diverse and widespread Class II transposable elements. Within the larger assemblage, the mariner-like elements (MLEs) and the Tc1-like elements (TLEs) are distinct families differing characteristically in the composition of the "D,D(35)E" cation-binding domain. Based on levels of sequence similarity, the elements in each family can be subdivided further into several smaller subfamilies. MLEs and TLEs both have an extraordinarily wide host range. They are abundant in insect genomes and other invertebrates and are found even in some vertebrate species including, in the case of mariner, humans, in which one element on chromosome 17p has been implicated as a hotspot of recombination. In spite of the extraordinary evolutionary success of the elements, virtually nothing is known about their mode of regulation within genomes. There is abundant evidence that the elements are disseminated to naive host genomes by horizontal transmission, and there is a substantial base of evidence for inference about the subsequent population dynamics. Studies of engineered mariner elements and induced mutations in the transposase have identified two mechanisms that may be operative in mariner regulation. One mechanism is overproduction inhibition, in which excessive wild-type transposase reduces the rate of excision of a target element. A second mechanism is dominant-negative complementation, in which certain mutant transposase proteins antagonize the activity of the wild-type transposase. The latter process may help explain why the vast majority of MLEs in nature undergo "vertical inactivation" by multiple mutations and, eventually, stochastic loss. There is also evidence that mariner/Tc1 elements can be mobilized in hybrid dysgenesis; in particular, certain dysgenic crosses in Drosophila virilis result in mobilization of a TLE designated Paris as well as the mobilization of other unrelated transposable elements.

Animals↗
PubMed1999

Development of a monitoring network for the analysis of elements in aerosol samples collected at Lake Balaton.

Determination of different toxic elements in aerosol and precipitation samples collected at Lake Balaton were carried out. A simple sequential leaching procedure was applied for the determination of the distribution of elements. The distribution of elements was determined among environmentally mobile, bound to carbonates and oxides, and bound to silicates and organic matters (environmentally immobile) fractions. Particular attention was paid to distinguish between environmentally mobile and environmentally immobile fractions because these represent the two extreme modes by which the metals are bound to the solid matrices. Aerosol samples were weekly collected in Tihany, Siófok and Keszthely on 5 cm diameter Teflon filters with a membrane pump. While Cd-compounds have been found enormously in the environmentally mobile fractions, As-compounds accumulated almost evenly among portions. The results of sequential leaching give an indication of the mobility of the elements once the aerosol is mixed directly into natural waters on during scavenging of the aerosol by wet deposition. Based upon the data it can be concluded that the effect of anthropogenic sources is minor in this area.

Aerosols↗
PubMedDate not supplied

[Trace element composition of bone tissue of mice in the normal state and in hypokinesia].

Using neutron activation analysis, the concentration of 13 elements was measured in functionally different bones of mice: weight-bearing and dynamic femurs, essentially stationary temporal bones, and newly formed ectopis bones under the renal capsule developed at the site of implantation of syngenic bone marrow. It was found that the elementary composition of the above bones was different in the norm and that it varied in the course of 3-week hypokinesia produced by small-size cages. It was shown that during hypokinesia the elementary composition changed according to four different patterns. Progressive demineralization due to Ca, P, Mg and Fe losses was accompanied by compensatory incorporation of Sr. In the course of the hypokinetic stress the content of trace elements (Zn, Cr, Ru, Rb, Br, Co, Sb) varied significantly. The mechanisms of action of these elements was related to the mobilization of activating elements at different stages of the general adaptation syndrome.

Adaptation, Physiological↗
PubMed1998

Nested insertions of short mobile sequences in Drosophila P elements.

A potentially full-sized P element isolated from the genome of Drosophila ambigua by polymerase chain reaction amplification was completely sequenced. It has a length of 3329 bp and the termini are formed by 33 bp inverted repeats. Sequence comparisons show that it can be classified as a member of the T-type P element subfamily. The translational reading frames of all four exons are interrupted by stop codons and frameshift mutations. At the 3' end of exon 3 a 687 bp insertion sequence (IS-amb-P) is found that also occurs in the form of dispersed copies (IS-amb) in the genome in D. ambigua. At the interspecific level it shows homology to mobile sequences of other species of the obscura group. Although variable in length, these IS elements are characterized by conserved sections without coding function and by 14 bp inverted repeats, one at a terminal, the other at a subterminal position. In situ hybridization revealed that P elements in D. ambigua are restricted to only two euchromatic sites on chromosome elements A and E. This situation resembles that found in Drosophila guanche and Drosophila subobscura where P homologs are clustered at a single site on chromosome element E and where the section corresponding to exon 3 of P elements carries an IS element. The gene sik-hom, which is located at the 5' side of the D. guanche cluster of P homologs, was used as a marker to examine whether the P element sites on chromosome element E of D. guanche and D. ambigua are homologous. The results suggest that the nested insertions of IS elements into P elements must have occurred independently in the two different lineages.

Amino Acid Sequence↗
PubMed1999

SR2 elements, non-long terminal repeat retrotransposons of the RTE-1 lineage from the human blood fluke Schistosoma mansoni.

As in other eukaryotes, a substantial portion of the genome of the human blood flukes belonging to the genus Schistosoma appears to be composed of mobile genetic elements and other repetitive sequences. The constitutent elements and their relative organization are not well understood, although retroposons (the SM alpha elements) and a family of non-long terminal repeat (LTR) retrotransposons (the SR1 elements) have been reported from the genome of Schistosoma mansoni. Here, we report the presence of a second family of non-LTR retrotransposons from S. mansoni which we have termed the SR2 elements. SR2 elements are members of a recently described lineage of non-LTR retrotransposons typified by the RTE-1 non-LTR retrotransposon of Caenorhabditis elegans. We determined the sequence for approximately 3.9 kb of a consensus full-length SR2 element, which included a long 5' untranslated region (UTR), potential first and second open reading frames (ORFs) of 78 and 1,018 amino acid residues, respectively, a short 3' UTR, and an A-rich 3' terminus. SR2 elements were bound by target site duplications. The putative first and second ORFs did not overlap. The second ORF was homologous to retroviral pol and encoded an apurinic/apyrimidinic endonuclease and a reverse transcriptase. A number of extremely short SR2 elements of less than 0.5 kb, reminiscent of SINEs, were also characterized. These consisted solely of the 5' and 3' UTRs of full-length SR2 elements, having both ORFs deleted. Analysis indicated that these SINE-like SR2 elements were produced by replication of a SINE-like SR2 element, rather than by repeated deletions within larger SR2 elements.

Amino Acid Sequence↗
PubMed1993

Cloning and sequence analysis of the 5'-flanking region of the estrogen sulfotransferase gene: steroid response elements and cell-specific nuclear DNA-binding proteins.

A 2954 bp region of the guinea pig estrogen sulfotransferase gene was cloned and sequenced including 2888 nt upstream of the cap site. This represents the first cloning of the promoter region of a steroid sulfotransferase gene. The 5'-flanking region was found to contain a conventional TATA box variant and sequences homologous to estrogen and glucocorticoid response elements. Gel mobility shift assays detected the presence of nuclear proteins in adrenocortical SW-13 and Y-1 cells that bind specifically to 30 mer DNA sequences containing either estrogen or glucocorticoid response elements. In contrast, gel shift experiments using 3T3 fibroblast cells failed to demonstrate similarly upshifted bands. Block deletion studies indicated that regulation of basal estrogen sulfotransferase promoter activity was located within the first 1000 bp upstream of the transcription initiation site.

Adrenal Cortex↗
PubMed2005

Macrolide inactivation gene cluster mphA-mrx-mphR adjacent to a class 1 integron in Aeromonas hydrophila isolated from a diarrhoeic pig in Oklahoma.

OBJECTIVES: To characterize a multidrug-resistant Aeromonas hydrophila isolate (CVM861) that possesses a high-level macrolide inactivation gene cluster (mphA-mrx-mphR), previously only reported in Escherichia coli. METHODS: PCR fragment length mapping, gene sequencing and Southern blotting were used to map the mphA-mrx-mphR gene cluster and flanking elements in CVM861. Conjugation experiments were done to determine whether the multidrug resistance genetic element was mobile. RESULTS: The mphA-mrx-mphR gene cluster mapped downstream of a class 1 integron and upstream of an aph(3') gene, and was present on a Tn21-like element. The gene order determined by sequencing was intI1-dhfrXII-orfF-aadA2-qacDeltaE-sul1-orf5Delta178-tnpA-mphR-mrx-mphA. Horizontal transmission of high-level macrolide resistance from CVM861 to E. coli 47011 was inconsistent; however, a composite plasmid possessing the mphA gene cluster was transferred at a conjugation frequency of 2.02 x 10(-5) per recipient. CONCLUSIONS: An mphA-mrx-mphR gene cluster was present downstream of the In2 integron located on a Tn21-like transposon in an A. hydrophila isolate. Whether this recombination event resulted in the truncation of the orf5 sequence is unknown. The presence of other resistance genes downstream of the mphA-mrx-mphR gene cluster suggests that multiple recombination events have occurred on this genetic element. This is the first known report of the mphA-mrx-mphR gene cluster carried by A. hydrophila and the first known isolation of this cluster in the United States.

Aeromonas hydrophila↗
PubMed1995

Transposon signatures: species-specific molecular markers that utilize a class of multiple-copy nuclear DNA.

Transposable elements are mobile sequences found in nuclear genomes and can potentially serve as molecular markers in various phylogenetic and population genetic investigations. A PCR-based method that utilizes restriction site variation of element copies within a genome is developed. These patterns of site variation, referred to as transposon signatures, are useful in differentiating between closely related groups. Signature data using the magellan retrotransposon, for example, is useful in examining relationships within the genus Zea and Tripsacum. This method allows transposable elements, or even other multiple-copy nuclear DNA sequences, to be generally utilized as molecular markers in discriminating between other closely related species and subspecies.

Base Sequence↗
PubMed1991

Convergent transcription initiates from oppositely oriented promoters within the 5' end regions of Drosophila melanogaster F elements.

Drosophila melanogaster F elements are mobile, oligo(A)-terminated DNA sequences that likely propagate by the retrotranscription of RNA intermediates. Plasmids bearing DNA segments from the left-hand region of a full-length F element fused to the CAT gene were used as templates for transient expression assays in Drosophila Schneider II cultured cells. Protein and RNA analyses led to the identification of two promoters, Fin and Fout, that transcribe in opposite orientations. The Fin promoter drives the synthesis of transcripts that initiate around residue +6 and are directed toward the element. Fin, that probably controls the formation of F transposition RNA intermediates and gene products, is internal to the transcribed region. Sequences important for accumulation of Fin transcripts are included within the +1 to +30 interval; an additional regulatory element may coincide with a heptamer located downstream of this region also found in the 5' end regions of F-like Drosophila retrotransposons. Analysis of the template activity of 3' deletion derivatives indicates that the level of accumulation of Fin RNA is also dependent upon the presence of sequences located within the +175 to +218 interval. The Fout promoter drives transcription in the opposite orientation with respect to Fin. Fout transcripts initiate at nearby sites within the +92 to +102 interval. Sequences downstream of these multiple RNA start sites are not required for the activity of the Fout promoter. Deletions knocking out the Fin promoter do not impair Fout transcription; conversely, initiation at the Fin promoter still takes place in templates that lack the Fout promoter. At a low level, both promoters are active in cultured cells.

Animals↗
PubMed1989

A subsequence-specific DNA-binding domain resides in the 13 kDa amino terminus of the bacteriophage Mu transposase protein.

We have previously reported that the 13 kDa amino terminus of the 70 kDa bacteriophage D108 transposase protein (A gene product) contains a two-component, sequence-specific DNA-binding domain which specifically binds to the related bacteriophage Mu's right end (attR) in vitro. To extend these studies, we examined the ability of the 13 kDa amino terminus of the Mu transposase protein to bind specifically to Mu attR in crude extracts. Here we report that the Mu transposase protein also contains a Mu attR specific DNA-binding domain, located in a putative alpha-helix-turn-alpha-helix region, in the amino terminal 13 kDa portion of the 70 kDa transposase protein as part of a 23 kDa fusion protein with beta-lactamase. We purified for this attR-specific DNA-binding activity and ultimately obtained a single polypeptide of the predicted molecular weight for the A'--'bla fusion protein. We found that the pure protein bound to the Mu attR site in a different manner compared with the entire Mu transposase protein as determined by DNase I-footprinting. Our results may suggest the presence of a potential primordial DNA-binding site (5'-PuCGAAA-3') located several times within attR, at the ends of Mu and D108 DNA, and at the extremities of other prokaryotic class II elements that catalyze 5 base pair duplications at the site of element insertion. The dissection of the functional domains of the related phage Mu and D108 transposase proteins will provide clues to the mechanisms and evolution of DNA transposition as a mode of mobile genetic element propagation.

Bacteriophage mu↗
PubMed1999

Nuclear factor-kappa B mediates TNF-alpha inhibitory effect on alpha 2(I) collagen (COL1A2) gene transcription in human dermal fibroblasts.

Among its plethora of activities as an inflammatory mediator, TNF-alpha has potent regulatory control on extracellular matrix production and degradation. Earlier studies have documented that TNF-alpha inhibits type I collagen gene (COL1A2) expression at the transcriptional level, but the characterization of the transcription factors involved has been elusive. In the present study, using transient cell transfection of human dermal fibroblasts with a battery of 5' end deletion/chloramphenicol acetyltransferase (CAT) reporter gene constructs, we have characterized the TNF-alpha response element of the COL1A2 promoter. The TNF-alpha response element was attributed to a specific region that comprises noncanonical activator protein-1 (AP-1) (CGAGTCA) and NF-kappa B (AGAGTTTCCC) binding sites. TNF-alpha effect was eliminated by a 2-bp substitution mutation in the NF-kappa B1 binding half site of the NF-kappa B cis element. Electrophoretic mobility shift assays (EMSA) showed that recombinant human NF-kappa B heterodimers as well as NF-kappa B1 and RelA homodimers, but not AP-1, were capable of binding this element. Further, EMSA with human fibroblast nuclear extracts demonstrated enhanced binding of a single, specific complex within 5 min of TNF-alpha stimulation, which reached a plateau by 1 h and was not affected by preincubation of cells with cycloheximide. Gel supershift assays identified the complex as the NF-kappa B (p50/p65) heterodimer, whereas Abs to nuclear factor of activated T cells (NF-AT) and Jun family members failed to recognize the complex. These data suggest that in fibroblasts TNF-alpha activates and initiates the nuclear translocation of NF-kappa B that binds a divergent NF-kappa B element and plays a critical role in the observed inhibition of alpha 2(I) collagen gene transcription.

Carrier Proteins↗
PubMed2003

Speciation and transport of heavy metals and macroelements during electroremediation.

Electroremediation makes treatment of contaminated clay soils possible. The external electrical field causes several transport processes and changes in soil chemistry. This study concerns the leachability and transport of calcium, magnesium, copper, zinc, lead, nickel manganese, chromium, and iron during treatment with an electric field of soil from a chlor-alkali factory. As expected, most elements were removed from the acidic part of the soil and accumulated in the zone where pH changed from acidic to alkaline. However, acidic leaching of the soil in this zone did not mobilize the elements. Lead formed both an anionic complex which electromigration transported toward the anode as well as a cationic lead fraction which moved toward the cathode. The anionic complex could be lead sulfate. Lead from both fractions was strongly attached to the soil after treatment. The low availability of metals and macroelements after electrokinetic remediation could make electroremediation, excavation, and deposition of the accumulation zone an alternative for the treatment of contaminated soils.

Electrochemistry↗
PubMed2000

Frequent human genomic DNA transduction driven by LINE-1 retrotransposition.

Human L1 retrotransposons can produce DNA transduction events in which unique DNA segments downstream of L1 elements are mobilized as part of aberrant retrotransposition events. That L1s are capable of carrying out such a reaction in tissue culture cells was elegantly demonstrated. Using bioinformatic approaches to analyze the structures of L1 element target site duplications and flanking sequence features, we provide evidence suggesting that approximately 15% of full-length L1 elements bear evidence of flanking DNA segment transduction. Extrapolating these findings to the 600,000 copies of L1 in the genome, we predict that the amount of DNA transduced by L1 represents approximately 1% of the genome, a fraction comparable with that occupied by exons.

3' Untranslated Regions↗
PubMed1994

Insertions of IS256-like element flanking the chromosomal beta-lactamase gene of Enterococcus faecalis CX19.

We have previously identified an inverted repeat characteristic of staphylococcal beta-lactamase transposons adjacent to the chromosomal beta-lactamase genes of Enterococcus faecalis CH19 and its beta-lactamase-producing transconjugant CX19. Nucleotide sequence analysis of the CH19 beta-lactamase structural gene (blaZ) reveals it to be identical to the blaZ gene from E. faecalis HH22 and to the blaZ gene from the staphylococcal beta-lactamase transposon Tn552. We also report the presence of nucleotide sequence identical to a 317-bp region of the staphylococcal insertion sequence IS256 upstream of the blaZ gene in both CH19 and CX19. The identical segment of IS256 is present downstream of the blaZ gene of CX19, suggesting a second insertion of the element (in the inverted orientation) accompanying transfer to the recipient strain. Restriction analysis of the areas beyond the ClaI sites used to clone these regions suggests that full copies of the IS256-like element (designated IS256E) are present in all positions but that these elements were not directly involved in the transfer of the beta-lactamase gene to the recipient strain. We have also identified a region downstream of the second IS256E insertion site which exhibits substantial homology to ISSIW, an iso-ISSI insertion originally identified in Lactococcus lactis subsp. cremoris. These data suggest that the two enterococcal blaZ genes sequenced to date evolved from a common ancestor and may at one time have been incorporated into a transposon similar to Tn552. They also suggest that IS256-like elements are mobile in E. faecalis and capable of inserting in a manner consistent with the formation of novel composite transposons. Finally, they provide the first confirmation of the presence of an ISSI-like element in enterococci, raising the possibility that these elements play a role in the exchange of chromosomal antimicrobial resistance determinants.

Base Sequence↗
PubMed1998

Unusual insertion element polymorphisms in the promoter and terminator regions of the mucAB-like genes of R471a and R446b.

We have previously identified umu-complementing genes on two incL/M plasmids, R471a and R446b (C. Ho et al., J. Bacteriol., 175 (1993) 5411-5419). Molecular analysis of these genes revealed that they are more structurally and functionally related to mucAB from the incN plasmid pKM101 than to other members of the previously identified Umu-like family. As a consequence, we have termed these new homologs mucAB(R471a) and mucAB(R446b) respectively. Interestingly, while the location of the mucAB-like genes is essentially the same in both R471a and R446b, the regions immediately flanking the mucAB-like genes are highly polymorphic. For example, 5' to mucAB(R471a) we found an insert that appears to be a novel retroelement encoding a putative reverse transcriptase (RT). This RT is related to the reverse transcriptases encoded by group II introns but is embedded in a retron-like context. Immediately 3' to the mucAB(R471a) locus is a putative insertion element of a sparsely-dispersed class not previously reported from enteric bacteria. Both the RT and insertion element are absent in R446b. These observations suggest that the mucAB-like genes from R471a and R446b are located within regions of the R-plasmids that perhaps were once (or still are) mobile genetic elements. Such observations might help explain the distribution of umu-like genes on R-plasmids and bacterial chromosomes.

Amino Acid Sequence↗
PubMed1999

Genomic structure and ecdysone regulation of the prophenoloxidase 1 gene in the malaria vector Anopheles gambiae.

Prophenoloxidase, a melanin-synthesizing enzyme, is considered to be an important arthropod immune protein. In mosquitoes, prophenoloxidase has been shown to be involved in refractory mechanisms against malaria parasites. In our study we used Anopheles gambiae, the most important human malaria vector, to characterize the first arthropod prophenoloxidase gene at the genomic level. The complete nucleotide sequence, including the immediate 5' flanking sequence (-855 bp) of the prophenoloxidase 1 gene, was determined. The gene spans 10 kb and is composed of five exons and four introns coding for a 2.5-kb mRNA. In the 5' flanking sequence, we found several putative regulatory motifs, two of which were identified as ecdysteroid regulatory elements. Electrophoretic mobility gel-shift assays and supershift assays demonstrated that the Aedes aegypti ecdysone receptor/Ultraspiracle nuclear receptor complex, and, seemingly, the endogenous Anopheles gambiae nuclear receptor complex, was able to bind one of the ecdysteroid response elements. Furthermore, 20-hydroxyecdysone stimulation was shown to up-regulate the transcription of the prophenoloxidase 1 gene in an A. gambiae cell line.

Animals↗
PubMed1995

Binding of Escherichia coli integration host factor (IHF) to the origin segment of p15A plasmid.

The integration host factor (IHF) is a sequence-specific, histone-like, multi-functional DNA-binding and -bending protein of Escherichia coli. Characterization and functional analysis of this protein has been carried out mainly in bacteriophage lambda and other mobile genetic elements. In this paper we report data concerning the binding of IHF protein to the plasmid orip15A region. IHF binds to the single site of the DNA fragment containing the orip15A, as shown by the gel mobility shift assays and footprinting experiment. On the basis of the ihf consensus sequences published, we have been able to identify one sequence of putative ihf site into the orip15A sequence with two mismatches in relation to the consensus sequence of Kur et al., 1989, Gene 81, 1-15. One ihf binding site was also found in the oriColE1 region sequence with three mismatches in relation to this consensus sequence.

Bacterial Proteins↗