Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A minimal mechanism is proposed which describes the transcriptional and translational processes for four phage proteins (RNA polymerase, DNase, primase and DNA polymerase) involved in T3/T7 DNA replication. Phage DNA replication is also included. It is shown how lag times may be incorporated into a kinetic mechanism. The distinct three-stage transport of phage DNA into the bacterial host (E. coli) is considered. DNA transport is assumed to be rate-determining for the transcription of class I and II proteins. Transcriptional and translational lag times have been calculated on the basis of available gene mapping of T7 phages. The kinetic behavior of T7 and T3 phage infection is practically identical. The hydrolysis of bacterial DNA by phage DNase (endonculease and exonuclease) as well as the subsequent phosphorylation to the deoxymononucleoside triphosphates are assumed to be rate-determining in phage DNA replication. Good agreement with experiment is obtained in our computer simulations.
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PMID:Computer simulation of T3/T7 phage infection using lag times. 330 Aug 7

We have obtained polyamine-compacted DNA and analyzed it by electron microscopy employing the method described by Dubochet, suitable for the study of complexes in which the main interactions are of ionic character. In addition, we have developed a simple biochemical method, based on the action of pancreatic DNase I, to demonstrate the condensation of DNA with spermidine. DNA-spermidine complexes are resistant to the action of DNase I, and there is a strong correlation between the presence of condensed DNA forms, both as toroids and as cylinders, and the insensitivity to DNase I activity. We have also shown that pBR322 DNA-spermidine complexes are transcriptionally active in the presence of Escherichia coli RNA polymerase. This supports the data concerning the biological activity of spermidine-condensed DNA.
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PMID:Electron microscopy and biochemical properties of polyamine-compacted DNA. 332 79

The human ribosomal RNA promoter contains two distinct control elements (UCE and core) both of which are recognized by the sequence-specific DNA binding protein UBF1, which has now been purified to apparent homogeneity. The purified factor activates RNA polymerase I (RNA pol I) transcription through direct interactions with either control element. A second RNA pol I transcription factor, designated SL1, participates in the promoter recognition process and is required to reconstitute transcription in vitro. Although SL1 alone has no sequence-specific DNA binding activity, deoxyribonuclease I footprinting experiments reveal that a cooperative interaction between UBF1 and SL1 leads to the formation of a new protein-DNA complex at the UCE and core elements. In vitro transcription experiments indicate that formation of the UBF1-SL1 complex is vital for transcriptional activation by UBF1. Thus, protein-protein interactions between UBF1 and SL1 are required for targeting of SL1 to cis-control sequences of the promoter.
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PMID:Functional cooperativity between transcription factors UBF1 and SL1 mediates human ribosomal RNA synthesis. 341 83

The mammalian activator protein ATF stimulates transcription from the adenovirus E4 promoter by binding to multiple upstream promoter and enhancer elements. DNAase footprint analyses have revealed that there are cooperative interactions between ATF and TFIID (the mammalian TATA factor) when both are bound simultaneously to the promoter and that these interactions in turn facilitate promoter recognition by RNA polymerase II and the general initiation factors TFIIB and TFIIE. However, the complex of TFIID and the other general factors is stable following oligonucleotide-mediated dissociation of ATF from the complete preinitiation complex. These results indicate that TFIID is a direct target for ATF, that these interactions facilitate assembly of a complete preinitiation complex, and that the role of ATF might be transient.
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PMID:Transcription factor ATF interacts with the TATA factor to facilitate establishment of a preinitiation complex. 341 54

In the accompanying paper (Horikoshi et al., 1988) the interaction between ATF and the general transcription initiation factors was analyzed by DNAase I footprinting experiments. Here, we use transcription assays to investigate the role of ATF in the assembly of a functional preinitiation complex. Addition of an oligonucleotide containing an ATF binding site inhibits E4 transcription by sequestering ATF. However, following preincubation of the E4 promoter in the nuclear extract, transcription is refractory to inhibition by the ATF oligonucleotide. Formation of this oligonucleotide-refractory complex occurs at an early stage in the overall transcription initiation reaction and is dependent upon ATF and the general transcription factors RNA polymerase II, TFIIB, and TFIID. This latter result suggests that the assembly and maintenance of a functional preinitiation complex involves cooperative interactions among the various transcription factors. The general transcription factor TFIIE, although required for transcriptional activity, is not involved in the assembly of an ATF oligonucleotide-refractory complex. Our results support the possibility that ATF may be required only transiently for assembly of a functional preinitiation complex.
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PMID:Analysis of the role of the transcription factor ATF in the assembly of a functional preinitiation complex. 341 55

The DNAase I sensitivities of the somatic-type 5 S DNA and oocyte-type 5 S DNA have been compared in nuclei from adult somatic tissues of Xenopus laevis. Neither of these Type III genes is expressed in mature erythrocytes and only somatic-type 5 S DNA is expressed in liver. We find that somatic-type 5 S DNA is DNAase-I-sensitive in liver nuclei and less sensitive in erythrocyte nuclei, while oocyte-type 5 S DNA is insensitive in both tissues. The DNAase I sensitivity appears to be uniform across each active somatic-type 5 S DNA repeat. Two regions slightly hypersensitive to DNAase I are found only in liver somatic-type 5 S DNA. One of these regions is within the gene, overlapping with the binding site of the transcription factor (TF III A) required for 5 S RNA synthesis. Thus, the correlation between DNAase I sensitivity and gene activity previously seen for protein-coding genes also holds for these Type III genes. Our data lead us to suggest that the fully DNAase-I-sensitive chromatin conformation on 5 S DNA requires the presence both of transcription factors and RNA polymerase.
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PMID:DNAase I sensitivities in chromatin of the Xenopus laevis somatic and oocyte 5 S DNAs. 356 98

[35S]Methionine-labeled proteins from total or cytoplasmic extracts of Vero cells infected with African swine fever virus were chromatographed on native and denatured DNA-cellulose and DNA-binding proteins were analyzed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), by DNA binding to Western blots, or by two-dimensional electrophoresis. Thirteen virus-specific DNA-binding proteins were detected by one-dimensional analysis. Major species have molecular mass 44,000 (44K), 38K, 20K, 18K, 14K, 13K, and 12K. The remaining DNA-binding proteins are proteins with molecular mass 130K, 110K, 35K, 33K, 17K, and 14.5K. When viral DNA used in the binding assay the results were very similar but the 13K protein did not bind viral DNA. Seven other minor virus-specific DNA-binding proteins could be detected by two-dimensional analysis. This technique also enabled the assignment of virus-specific proteins. Seven of the virus-specific DNA-binding proteins are structural proteins. Twelve are late proteins, the remaining being early proteins synthesized before viral DNA replication. Most of the virus-specific DNA-binding proteins bind both to double-stranded and to single-stranded DNA. The 110K, 29K, and 18K DNA-binding proteins bind only to single-stranded DNA. Two virus-specific enzymatic activities, DNA polymerase and RNA polymerase, were present in the fractions separated by DNA-cellulose chromatography. The virus-specific single-stranded DNA nuclease did not bind to DNA.
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PMID:DNA-binding proteins specified by African swine fever virus. 368 26

The human rRNA promoter contains two distinct cis-control sequences, the core and upstream control element (UCE), that serve as the target for binding cellular trans-activating proteins involved in transcription initiation by RNA polymerase I. One of these factors, SL1, has been extensively purified and shown to be a species-specific factor required to reconstitute in vitro RNA synthesis. DNAase footprinting revealed that although SL1 alone does not bind specifically to rRNA promoter sequences, a second factor, UBF1, recruits SL1 to the template and directs binding to an extended region encompassing sequences in the UCE. Analysis of mutant and human-mouse hybrid promoters indicate that protein-DNA interactions at the UCE modulate the efficiency of rRNA synthesis. Transcription from the human rRNA promoter appears to require an unusual set of protein-DNA transactions in which recognition and binding to an upstream cis-control element is carried out by one factor (UBF1), whereas activation requires an additional factor, SL1, acting in conjunction with UBF1 to trigger transcription.
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PMID:Human rRNA transcription is modulated by the coordinate binding of two factors to an upstream control element. 370 92

Drosophila Kc cells were utilized to prepare nuclear extracts in which promoter-containing DNA templates were efficiently transcribed by RNA polymerase II. A combination of fractionation schemes was used to identify and partially purify seven activities (factors) which affected the transcription of four different genes in vitro. Reconstructing specific transcription required exogenous RNA polymerase II in addition to these factors. Moreover, the high efficiency of transcription characteristic of the crude extract was preserved in reconstruction reactions. The methods used are presented in detail. Functions were assigned to several of the factors. One essential factor appeared to affect initiation and displayed chromatographic properties unlike any other Drosophila transcription factor previously described. Two factors specifically affected RNA chain elongation. Another activity was a DNase inhibitor required to preserve template integrity in the fractionated system. The remaining three factors were not absolutely essential but affected the specific in vitro transcription either qualitatively or quantitatively. A comparison of these transcription factors with other Drosophila and mammalian transcription factors is made.
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PMID:Fractionation of transcription factors for RNA polymerase II from Drosophila Kc cell nuclear extracts. 381 40

A DNase protection technique is described and applied to the interaction of three lac control proteins with supercoiled lac DNA. The technique uses end-labeled oligonucleotide primers to probe specific DNA regions as an alternative to protocols requiring restriction endonuclease cleavage or blotting. Thus DNA may be probed with high resolution in its native state. It is demonstrated that the introduction of supercoiling into DNA accelerates the rate of lac ps promoter binding by RNA polymerase but does not alter the positions at which polymerase, c-AMP-binding protein, or lac repressor bind to lac DNA.
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PMID:Rapid "footprinting" on supercoiled DNA. 388 2


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