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The promoter-proximal KCS element of the PKR kinase gene enhances transcription irrespective of orientation and position relative to the ISRE element and is functionally distinct from the KCS-like element of the ADAR deaminase Promoter.

The RNA-dependent protein kinase PKR promoter is interferon (IFN) inducible and possesses a novel 15-base pair (bp) constitutive activator element, designated kinase conserved sequence (KCS), in addition to an IFN-stimulated response element (ISRE). Deletion of the KCS element or point mutations within the KCS element greatly reduce both basal and IFN-inducible PKR promoter activity. The IFN-inducible RNA-specific adenosine deaminase ADAR1 promoter possesses a KCS-like (KCS-l) element. The sequences of the KCS and KCS-l elements and their positions relative to the cognate ISRE element are similar between the PKR and ADAR1 promoters. However, substitution of the ADAR1 KCS-l element for the KCS element of the PKR promoter resulted in significantly reduced basal and IFN-inducible promoter activities comparable to either point mutation or entire deletion of the PKR KCS element. The PKR KCS element selectively bound nuclear proteins more efficiently than did the ADAR1 KCS-l element. Reversing the positions of the KCS and ISRE elements of the PKR promoter relative to one another or reversing the orientation of either element while conserving the naturally occurring 4-bp spacing between the two elements did not significantly reduce basal or IFN-inducible promoter activity. Taken together, these results are consistent with the notion that the KCS and ISRE elements of the PKR promoter function as a unit.

Adenosine Deaminase↗

Regulation of the interferon-inducible PKR kinase gene: the KCS element is a constitutive promoter element that functions in concert with the interferon-stimulated response element.

The RNA-dependent protein kinase PKR plays important roles in the antiviral and antiproliferative actions of IFN. The IFN-inducible promoter of the human PKR gene contains a 15-bp DNA element designated KCS. The KCS element is located 4 bp upstream of the interferon-stimulated response element (ISRE) and is required for both basal and IFN-inducible transcription. We have examined the effect of insertion mutations between the KCS and the ISRE elements, as well as altered orientation of the KCS element relative to the ISRE element, to assess a possible functional interaction between them. Large insertions (>or=93 bp) between the KCS and ISRE elements significantly reduced both basal and IFN-inducible promoter activity. The function of the KCS element was dependent on the orientation of KCS relative to the ISRE element. Multimerization of the KCS element increased both basal and IFN-inducible transcription. Electrophoretic mobility shift analyses (EMSA) identified IFN-inducible protein complex formation that required both the KCS and the ISRE DNA element sequences. The novel IFN-inducible protein complexes contained the transcription factor STAT1, as shown by supershift analyses and by their presence in extracts prepared from STAT1 wild-type but not from STAT1-/- null cells. These results, taken together, strongly suggest that the KCS and ISRE elements of the human PKR promoter represent a functional unit.

Animals↗

The Hermes transposable element from the house fly, Musca domestica, is a short inverted repeat-type element of the hobo, Ac, and Tam3 (hAT) element family.

The genome of the house fly, Musca domestica, contains an active transposable element system, called Hermes. Using PCR and inverse PCR we amplified and sequenced overlapping segments of several Hermes elements and from these data we have constructed a 2749 bp consensus Hermes DNA sequence. Hermes termini are composed of 17 bp imperfect inverted repeats that are almost identical to the inverted terminal repeats of the hobo element of Drosophila melanogaster. Full length Hermes elements contain a single long ORF capable of encoding a protein of 612 amino acids which is 55% identical to the amino acid sequence of the hobo transposase. Comparison of the ends of the Hermes and hobo elements to those of the Ac element of Zea mays, and the Tam3 element of Antirrhinum majus, as well as several other plant and insect elements, revealed a conserved terminal sequence motif. Thus Hermes is clearly a member of the hobo, Ac and Tam3 (hAT) transposable element family, other members of which include the Tag1 element from Arabidopsis thaliana and the Bg element from Zea mays. The evolution of this class of transposable elements and the potential utility of Hermes as a genetic tool in M. domestica and related species are discussed.

Amino Acid Sequence↗

Extrachromosomal elements of extrachromosomal elements of Paramecium and their extrachromosomal elements.

Expression of killer traits in Paramecium is due to a complex interaction between the lower eukaryote host and two or three elements that can be viewed either as extrachromosomal elements or as endosymbionts. In all cases, the determinants of the killer trait are carried by obligate bacterial endosymbionts belonging to the genus Caedibacter. However, the actual genetic determinants for expression of these traits are not an integral part of the symbiont genome. They are located on extrachromosomal genetic elements (plasmids or bacteriophages) which essentially are molecular endosymbionts of Caedibacter. In the case of the plasmids, they are associated with yet another set of extrachromosomal genetic elements, which are transposons. These transposons have been observed to move into new sites in the plasmids and even to disrupt expression of R body production and the killer trait. Thus, the transposons can be considered either as extrachromosomal elements of extrachromosomal elements (plasmids) of extrachromosomal elements (C. taeniospiralis) of paramecia, or as molecular parasites of molecular endosymbionts (plasmids) of bacterial endosymbionts of paramecia.

Animals↗

A human cytomegalovirus early promoter with upstream negative and positive cis-acting elements: IE2 negates the effect of the negative element, and NF-Y binds to the positive element.

The human cytomegalovirus early promoter for the UL4 gene, which codes for an early viral envelope glycoprotein designated gpUL4, requires immediate-early viral protein two (IE2) synthesis to be activated (C.-P. Chang, C. L. Malone, and M. F. Stinski, J. Virol. 63:281, 1989). We investigated the cis-acting and trans-acting factors that regulate transcription from this UL4 promoter. In transient transfection assays, the viral IE2 protein negated the effect of an upstream cis-acting negative element and enhanced downstream gene expression. A cis-acting positive element contributed to the activity of the viral promoter when an upstream cis-acting negative element was deleted or when the viral IE2 protein was present. The cellular protein(s) that binds to the cis-acting negative element requires further investigation. The cellular protein that binds to the cis-acting positive element was characterized. Two DNA sequence-specific protein complexes were detected with DNA probes spanning the region containing the cis-acting positive element and human cytomegalovirus-infected human fibroblast cell nuclear extracts. The more slowly migrating complex was labeled complex A, and the faster was labeled complex B. Only complex B was detected with mock-infected cell nuclear extracts. Competition experiments confirmed the specificity of the A and B complexes. The protein bound to the DNA in both the complexes contacts a CCAAT box imperfect dyad symmetry (5'CCAATCACTGG3'). Either CCAAT box within the dyad symmetry could compete for binding the nuclear factor. Mutation of the CCAAT box dyad symmetry resulted in a decrease of the transcriptional activity from the UL4 promoter. A cellular transcription factor, antigenically related to nuclear factor-Y (NF-Y), was found in both complexes A and B. Events associated with viral infection caused phosphorylation of protein complex A. Dephosphorylation of the DNA-binding protein converts complex A to complex B. The effect of phosphorylation of NF-Y is not known.

Acid Phosphatase↗

Ability of the glucocorticoid modulatory element to modify glucocorticoid receptor transactivation indicates parallel pathways for the expression of glucocorticoid modulatory element and glucocorticoid response element activities.

The glucocorticoid modulatory element (GME) of the rat tyrosine aminotransferase gene is located at -3.6 kb and 1 kb upstream of the glucocorticoid response elements (GREs). The GME has the unique transcriptional properties of modulating both the dose-response curve of agonists bound to the glucocorticoid receptor (GR) and the residual agonist activity of GR-bound antisteroids. The expression of GME activity involves the binding of two novel proteins (GMEB-1 and GMEB-2) that we have recently cloned. However, the mechanistic details are limited. The DNA sequence requirements for GME activity (CGTC) also remain poorly defined, which restricts efforts to identify other GME modulated genes. To help understand the mechanism for the unusual activities of the GME and to identify permissive gene environments for GME activity, we compared the changes in GME activity and GRE action (i.e. the fold induction by GR) caused by modifying several parameters. Phasing between the GME and downstream tandem GREs was unimportant, in contrast to other cis-acting elements like the GRE, while GME activity decreased rapidly when placed at increasingly larger distances 3' to a tandem GRE. A minimal promoter was less effective in supporting GME than GRE activity. Although CREB binds to the GME, overexpression of CREB reduced GRE, but not GME, activity and a CRE was inactive when substituted for the GME. No effect of the GME was observed on the binding of GRs to a single GRE. However, the GME upstream of a single GRE was also unable to produce a left shift in the Dex dose-response curve under conditions where the GME was active with two GREs. In the absence of any GREs, the GME displayed intrinsic activity by elevating basal level expression. Collectively, these results indicate that an optimal position for a functional GME is within 250 bp upstream of a tandem GRE driving a complex promoter. Furthermore, as the changes in GME activity did not correlate with those for fold induction from the GRE, the mechanisms for expression of GME and GRE activities appear to utilize parallel, as opposed to common pathways.

Animals↗

Identification and characterization of a versatile retinoid response element (retinoic acid receptor response element-retinoid X receptor response element) in the mouse tissue transglutaminase gene promoter.

Tissue transglutaminase (transglutaminase type II) is an intracellular protein cross-linking enzyme that accumulates in connective tissue and in cells undergoing apoptosis. Retinoids regulate the transcription of the mouse tissue transglutaminase gene via activation of regulatory elements contained within 4 kilobases of the 5'-end of the gene. Co-transfection studies with retinoid receptor expression vectors in CV-1 cells demonstrated that the mouse tissue transglutaminase promoter is activated by ligand activation of either retinoic acid receptor-retinoid X receptor (RAR.RXR) heterodimers or RXR homodimers. Optimal induction is achieved with retinoid receptor panagonists; partial activation can also be achieved with either RAR-specific or RXR-specific retinoids. Retinoid-dependent activation of the tissue transglutaminase promoter depends on both a proximal regulatory region containing sequences highly conserved between the human and the mouse tissue transglutaminase promoters and a distal region that includes a 30-base pair retinoid response element (mTGRRE1). mTGRRE1 contains three hexanucleotide half-sites (two canonical and one non-canonical) in a DR7/DR5 motif that bind both RAR*RXR heterodimers and RXR homodimers. These studies suggest that retinoid-dependent expression of the mouse tissue transglutaminase gene is mediated by a versatile tripartite retinoid response element located 1.7 kilobases upstream of the transcription start site.

3T3 Cells↗

Involvement of multiple cis elements in basal- and alpha-adrenergic agonist-inducible atrial natriuretic factor transcription. Roles for serum response elements and an SP-1-like element.

In the present study, cis elements in the 5'-flanking sequence (FS) of the rat atrial natriuretic factor (ANF) gene involved in regulating basal and alpha 1-adrenergic-inducible transcription were investigated. Truncation analyses using ANF-luciferase reporter constructs transfected into primary neonatal rat cardiac myocytes showed that an A/T-rich serum response element (SRE) at -114 bp of the ANF 5'-FS, which bound serum response factor (SRF), was required for basal and inducible transcription. In constructs composed of 134 bp of rat ANF 5'-FS driving luciferase (ANF-134Luc), mutations in the SRE at -114 bp disrupted SRF binding and ANF promoter activity. However, the same mutations in ANF-638Luc had little effect, suggesting a collaborating role for more distal sequences, such as the other SRE in ANF-638 at -406 bp. In ANF-638Luc, mutations in the SRE at -406 bp that disrupted SRF binding to that site decreased ANF reporter activity by only 25%; however, mutating both of the SREs completely blocked alpha 1-adrenergic-inducible activity. Mutation analyses showed that an ... (SP-1)-like site at -69 bp, shown previously to confer inducibility in reporters with 134 bp of ANF 5'-FS, was not required in ANF-638Luc. However, double mutants in the SP-1-like region and either SRE completely blocked alpha 1-adrenergic-inducible ANF promoter activity. These findings emphasize that no single element is responsible for alpha 1-adrenergic agonist-regulated ANF transcription but that the SREs at -114 and -406 bp and the SP-1-like sequence at -69 bp mediate the effect in collaboration.

Adrenergic alpha-Agonists↗

Beyond FIRO-B--three new theory-derived measures--Element B: behavior, Element F: feelings, Element S: self.

Although the FIRO-B instrument has been used widely for a large number of purposes, it was not designed as a general purpose instrument. Several years ago, after revising the FIRO theory underlying the instrument based on over 20 years' experience with the instrument and related activities, the author revised the FIRO-B extensively, so extensively it was given a new name, Element B. The new instrument is much stronger both theoretically and psychometrically while at the same time retaining the simplicity and shortness of the original. In addition, two new instruments based on the same theory were designed, developed, and tested. They measure feelings (Element F) and self-concept (Element S). All three instruments have, over the past 10 years, been used primarily as training instruments. When given in conjunction with other methods, they have been used for improving self-awareness, teamwork, morale, and productivity in such organizations as Procter & Gamble, AT&T, NASA, Amdahl Corporation, the Swedish Army, and about 100 companies in Japan. Included is a comment on scales anchored both logically, using methods such as facet design and unidimensional scaling, and empirically, such as the "big five."

Adult↗

Human placenta as a 'dual' biomarker for monitoring fetal and maternal environment with special reference to potentially toxic trace elements. Part 3: toxic trace elements in placenta and placenta as a biomarker for these elements.

The human placenta as a body component is exposed to several harmful substances, depending upon the environmental conditions encountered. In the case of toxic metals, placental tissue can be regarded as a dual biomarker to assess maternal and fetal health. The average range of concentrations for toxic trace elements in placenta based on wet weight are found to be: cadmium 1-6 ng/g; total mercury 2-13 ng/g; methyl mercury 1-14 microg/g; and lead 5-60 ng/g. The placenta appears to be at least a partial barrier for Cadmium. Cadmium transport includes a broad variety of mechanisms. Once in circulation, it mainly interferes with Ca and Zn transportation. On the other hand, placenta appears to be a weaker harrier for Pb than for Cd. In the case of Hg, predominantly the organic form is absorbed and readily crosses the placenta. In fetal blood, the organic mercury content is equal or even greater than in maternal blood, raising questions on normal fetal development. Placenta as a biomarker could be taken as an alternative to repeated maternal blood sampling for assessing lead exposure in utero. Placenta samples are usually obtained at the time of parturition, a one-time event. Hence, each pregnancy has to be looked upon as an RTM (real time monitoring) process since the affected species is exposed to the placental source of pollutants only during the course of that particular pregnancy.

Adult↗

The Biological System of the Elements (BSE). Part II: a theoretical model for establishing the essentiality of chemical elements. The application of stoichiometric network analysis to the biological system of the elements

Stoichiometric Network Analysis (SNA), originally developed by the Canadian chemist Bruce L. Clarke during the 1970s, provides a most efficient means of reducing the background topology of complex interaction networks to some skeleton topology around which systems dynamics can be understood without jeopardising insight into complex dynamics by over- or miss-simplification. Since it focuses on the corresponding autocatalytic (AC) features of a feedback system as those which control overall behaviour to some extent, SNA deals with reaction kinetics in and beyond chemistry, e.g. with nuclear reactions. It is therefore quite straightforward to apply this manner of simplification, which in turn is supported by a number of mathematical theorems on systems behaviour and properties of AC cycles, to biological systems although their 'full' complexity may not even be assessed in the yet rare cases of complete genetic sequencing. Assuming there is a relationship between the kinds of metal or metalloid species and key biological/biochemical transformations to be promoted with their aid--this relationship being the subject of bio-inorganic chemistry--and that biochemistry is, in effect, about systems which can reproduce and thus behave autocatalytically, one can expect SNA to yield formally sound statements on basic features of biology and biochemistry too. If we sum up the facts and considerations concerning essentiality or possible essentiality in a biological system of elements (Markert, 1994), this means joining the triangular representation of BSE, including statements on (the degree of biological) evolution and aggregation levels, to SNA treatment of autocatalysis within hierarchical systems from metalloenzymes to entire biocoenoses. Arguments using preferred cluster sizes and aggregation tendencies from coordination chemistry are then employed to circumscribe possible functions within the BSE. They are also extended to metals hitherto not known to be essential, such as tellurium or scandium.

Journal Article↗

Different evolutionary behaviour of P element subfamilies: M-type and O-type elements in Drosophila bifasciata and D. imaii.

Distribution and variation of two P-element subfamilies designated M-type and O-type elements were investigated in Drosophila bifasciata (Db) and its relatives. PCR screening revealed that full-sized and internally deleted elements of both types occur in three geographic Db strains and in the related species, D. imaii (Di). Molecular analyses indicate differences in the evolutionary behaviour of the two P-element types. Internally deleted M-type elements fall into two size classes present in all three Db strains. In contrast, internally deleted O-type elements vary between the strains in number and length. With respect to genomic location, M-type elements seem to be restricted to conserved euchromatic sites, whereas the positions of O-type elements appear to be geographically variable. In one strain of Db (Italy), O-type elements seem to accumulate in the heterochromatin. Sequencing of a 397-bp segment shows intra- and interspecific divergence of M-type elements. In a 452-bp segment of the O-type elements, no substitutions were found, neither within nor between species. This finding suggests recent introgression of O-type elements via hybridization between Db and Di. Sequence identity and variation in chromosomal locations among different copies imply that O-type elements are transpositionally active. For M-type elements, genomic mobility cannot be proved. In a survey of several other taxa, no O-type-related sequences were detected so far. Therefore, the origin of the O-type subfamily remains unknown, whereas the source of M-type elements can be traced back to the genus Scaptomyza.

Animals↗

Direct repeat 3-type element lacking the ability to bind to the vitamin D receptor enhances the function of a vitamin D-responsive element.

In a previous study, we identified the element which allows the maximum response to 1,25(OH)2D3 in concert with two vitamin D-responsive elements (VDREs) in the rat 25-hydroxyvitamin D3 24-hydroxylase gene promoter, and designated it an accessory element [Ohyama, Y., Ozono, K., Uchida, M., Yoshimura, M., Shinki, T., Suda, T. and Yamamoto, O. Functional assessment of two vitamin D-responsive elements in the rat 25-hydroxyvitamin D3 24-hydroxylase gene. J. Biol. Chem., 1996, 271, 30381-30385]. The accessory element located adjacent to the proximal VDRE is not capable of binding to the vitamin D receptor (VDR), while its nucleotide sequence resembles the consensus sequence of VDREs, direct repeat 3 (DR3). To clarify the difference between the accessory element and VDREs, the function of the accessory element was compared with that of VDREs. The mutated accessory elements with a single nucleotide substitution showed the capability of binding to the VDR in vitro. However, these mutants still did not act as a VDRE when driven by the heterologous SV40 promoter. The accessory element did not enhance the function of a cAMP-responsive element. The corresponding site of the accessory element in the human 24-hydroxylase is a DR4-type element, and this element did not function as an accessory element. These results indicate that a critical nucleotide sequence is necessary for the binding to the VDR and for mediating the vitamin D effect, and suggest the different regulation between the rat and human 24-hydroxylase gene.

8-Bromo Cyclic Adenosine Monophosphate↗

Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations.

The P transposable element copy numbers and the KP/full-sized P element ratios were determined in eight Brazilian strains of Drosophila melanogaster. Strains from tropical regions showed lower overall P element copy numbers than did strains from temperate regions. Variable numbers of full-sized and defective elements were detected, but the full-sized P and KP elements were the predominant classes of elements in all strains. The full-sized P and KP element ratios were calculated and compared with latitude. The northernmost and southernmost Brazilian strains showed fewer full-sized elements than KP elements per genome, and the strains from less extreme latitudes had many more full-sized P than KP elements. However, no clinal variation was observed. Strains from different localities, previously classified as having P cytotype, displayed a higher or a lower proportion of KP elements than of full-sized P elements, as well as an equal number of the two element types, showing that the same phenotype may be produced by different underlying genomic components of the P-M system.

Animals↗

P element mediated germ line transformation of Drosophila melanogaster with the Tc1 transposable DNA element from Caenorhabditis elegans.

Questions relating to the origin and regulation of mobile genetic elements are currently of considerable interest. Since it is now possible to address more precisely issues concerning the entry, dispersion, and regulation of elements within a virgin genome, one approach that may afford a better understanding of transposable elements in general could be provided by interspecific DNA transformation. Therefore, the Tc1 transposable DNA element from Caenorhabditis elegans was chosen as a proposed invading element of the Drosophila melanogaster genome. The basis for this selection resided in the inherent structural and functional similarities, as well as sequence identities, between the Caenorhabditis element and elements innate to Drosophila (e.g., P, HB1, and Uhu). Initial investigations were carried out to define a clone carrying an intact Tc1 element. This Tc1 element was inserted into a P transposon vector and two P-Tc1-ry+ constructs, differing only in insert orientation, were identified. P element mediated germ line transfer was then used to generate a transformant that was genetically and molecularly identified as containing a single, structurally intact Tc1 element at cytological location 64C4-5 on the third chromosome. The single P[(Tc1,ry+)]SAS-B insertion was thereafter mobilized by using a P[ry+ delta 2-3] element as a transposase source, and the genetic and molecular data suggested that the insertion had been successfully reintegrated to a variety of genomic locations. On the basis of genetic and molecular analyses, the Tc1 element in the P[Tc1,ry+)] transformed stock is not highly unstable in germ line and somatic tissues.

Animals↗

Three-dimensional finite element modelling of bone: effects of element size.

This study quantifies the effects of element size on the stress/strain results of finite element (FE) models of bone that are generated with a previously described automated method. This method uses cube-shaped hexahedral elements, which enabled element shape and aspect ratio to be held constant while the effects of element size were studied. Three models of a human proximal femur, each with a different element size (3.1 mm, 3.8 mm and 4.8 mm), were analysed. Convergence in strain energy of the models had been verified in previous work. The stresses and strains predicted by the models were compared on a pointwise basis using linear regression analysis. There was a general decrease in the level of stress and strain when element size was increased, even though convergence in strain energy had been achieved. An increase in element width from 3.1 mm to 3.8 mm decreased the predicted stresses by 13% to 29% overall; the predicted strains decreased by 4% to 20% for the same increase in element size. These results indicate that linear cube-shaped hexahedral elements must be very small (3 mm on a side or smaller) to represent the sharp variations in mechanical properties that exist in bone, and that use of larger elements decreases the predicted stresses and strains. The elements used in this study are similar to those typically used to represent trabecular bone in conventional (non-automated) FE modelling methods. Therefore, the sensitivity of the stress/strain results to element size that was found for trabecular bone also applies to conventional modelling of such bone.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?

An in silico search for P-transposable-element-related sequences in the Drosophila melanogaster genome allowed us to detect sequences that are similar to P-element transposases. These sequences are located in the central region of 3.4-kb Hoppel elements, a class II transposon. Polymerase chain reaction (PCR) analysis of the insertional polymorphism revealed that these elements are mobile. The 3.4-kb elements are the longest copies of this family ever found. They contain an open reading frame that is long enough to encode a transposase, suggesting that the 3.4-kb elements are the full-length copies of the Hoppel family. Multiple alignments of several P-element transposases from different species and the Hoppel-element-encoded peptide showed that all of the P-element introns and the 5' region of the transposase are absent from the Hoppel sequence. Sequence analysis combined with reverse transcriptase PCR analysis showed that the 3.4-kb Hoppel elements are intronless. P and Hoppel not only share similar amino acid sequences but also have terminal inverted repeats of the same length (31 bp), and their excision footprints present a similar structure, which suggests that their transposases are functionally very similar. Thus, we propose that the Hoppel element family be included in the P-element superfamily. Two evolutionary scenarios are discussed considering the presence /absence of introns within the P-element superfamily.

Amino Acid Sequence↗

P-element-induced male recombination can be produced in Drosophila melanogaster by combining end-deficient elements in trans.

Male recombination, not normally present in Drosophila melanogaster, can be produced at high rates when target P elements at homologous sites are combined in the presence of transposase protein. We have produced a set of elements by in situ deletion of a particular insertion and have found elements that have deletions stretching into either end. Elements were tested in pairs to see whether they complement each other in their ability to induce recombination. The combination of elements that are deficient for the same end produces very little recombination, but the combination of a right-end and a left-end element can generate recombination values higher than given by two complete P[CaSpeR] elements at homologous sites. This strongly suggests that "hybrid" P elements, containing ends from two different elements, can be recognized by transposase protein. We have also examined genotypes containing a normal and an end-deficient element and found that they yield reasonably high levels of recombination. We interpret the resultant gametes from such genotypes as showing that the majority of events in this genotype derive from the association of complementary ends from the same element, whereas the complementary ends from elements in trans associate in only a minority of cases.

Animals↗