Stable Elongation Complex Research Articles

Reversible Phosphorylation of the C-terminal Domain of RNA Polymerase II

Reversible Phosphorylation of the C-terminal Domain of RNA Polymerase II

The Photoactivated Cross-linking of Recombinant C-terminal Domain to Proteins in a HeLa Cell Transcription Extract That Comigrate with Transcription Factors IIE and IIF

The C-terminal domain (CTD) of RNA polymerase II (RNAP II) is essential for the assembly of RNAP II into preinitiation complexes on some promoters such as the dihydrofolate reductase (DHFR) promoter. In addition, during the transition from a preinitiation complex to a stable elongation complex, the CTD becomes heavily phosphorylated. In this report, interactions involving the CTD have been examined by protein-protein cross-linking. As a prelude to the study of CTD interactions, the effect of recombinant CTD on in vitro transcription was examined. The presence of recombinant CTD inhibits in vitro transcription from both the DHFR and adenovirus 2 major late promoters, suggesting that the CTD is involved in essential interactions with a general transcription factor(s). Factors in the transcription extract that interact with the CTD were identified by protein-protein cross-linking. Recombinant CTD was phosphorylated at its casein kinase II site, at the C terminus of the CTD, in the presence of [35S]adenosine 5'-O-(thiotriphosphate) and alkylated with azidophenacyl bromide. Incubation of azido-modified 35S-labeled CTD with a HeLa transcription extract followed by ultraviolet irradiation results in the covalent cross-linking of the CTD to proteins in contact with the CTD at the time of irradiation. Subsequent incubation with phenylmercuric acetate results in the transfer of 35S from the CTD to the protein to which it was cross-linked. The two major photolabeled bands have a M(r) of 34,000 and 74,000. The specificity of CTD interactions was demonstrated by a reduction in photolabeling in the presence of unmodified CTD or RNAP II containing an intact CTD (RNAP IIA) but not in the presence of a CTD-less RNAP II (RNAP IIB). The 35S-labeled 34- and 74-kDa proteins comigrate on SDS-polyacrylamide gel electrophoresis with the beta subunit of transcription factor IIE and the 74-kDa subunit of transcription factor IIF, respectively. Moreover, some of the minor 35S-labeled bands comigrate with other subunits of the general transcription factors.

Termination and Slippage by Bacteriophage T7 RNA Polymerase

We have examined the termination efficiency of T7 and T3 RNA polymerases (RNAPs) at a variety of termination signals. In agreement with previous investigators we find that termination occurs after the synthesis of an RNA product with a stable secondary structure followed by a run of U residues. Stem-loop structures that lack a 3′ U-tract fail to terminate the phage enzyme. The distance (or the sequence) between the start site for transcription and the termination signal may also be important, as placing the terminator at different locations downstream from the promoter, or changing the promoter sequence, results in alterations in termination efficiency. We have explored termination at extended runs of homopolymers in the absence of an apparent stem-loop structure, and have observed that the enzyme terminates (inefficiently) when synthesizing U-rich transcripts, but not A- or C-rich transcripts. This is especially true at low concentrations of UTP. Strikingly, when an elongation complex (EC) encounters a dA-tract in the template strand it is able to slide on the template, resulting in the synthesis of products that have more or fewer U residues than predicted by the sequence of the DNA. This observation suggests that the formation of an RNA : DNA hybrid may be important to the lateral stability of the EC (its ability to maintain proper register with the DNA template). We have also explored the termination properties of a proteolytically nicked form of T7 RNAP. The nicked enzyme forms a less stable EC than the intact RNAP and dissociates more readily from the template in regions that encode inherently destabilizing RNAs (e.g. stem-loop structures, poly(U)-tracts). However, the nicked enzyme terminates less efficiently at the late T7 terminator (T7-TΦ) or at a termination signal in the human preproparathyroid hormone gene. These results suggest that termination is a highly specific event, and not merely a consequence of decreased stability of the EC. Our observations are not consistent with previous models of termination by the phage RNAP and indicate that revisions to these models may be required.

Studies on the interaction of T7 RNA polymerase with a DNA template containing a site-specifically placed psoralen cross-link: II. Stability and some properties of elongation complexes

We constructed a 66 base-pair DNA template capable of supporting transcription by T7 RNA polymerase. This template had a psoralen cross-link downstream from a T7 promoter such that a 36 (+1) nucleotide transcript was synthesized at the time the T7 polymerase came to a stop at the cross-link. The stability of elongation complexes formed on this template, and the effect of different factors that are known to affect polymerase-DNA interactions was investigated by non-denaturing gel electrophoresis and gel filtration chromatography. We found that an elongation complex could lose its RNA component but the T7 polymerase still remained attached to the DNA template for extended periods of time (at least up to 18 h). This type of an elongation complex, bereft of its nascent RNA transcript, is called a quasi-elongation complex. DNase I footprinting within gel slices indicated that the polymerase molecules were arrested at the psoralen cross-link on the DNA template in the quasi-elongation complexes. The quasi-elongation complexes were found to be extremely stable in 0.5 m-NaCl and in 0.2 m-NaCl plus 60m m-MgCl 2, and could withstand temperatures up to 42 °C. The quasi-elongation complexes were destabilized by heparin and excess calf thymus DNA. Excess tRNA caused only a minimal degree of disruption. Non-promoter-containing plasmid DNAs did not have a destabilizing effect on the quasi-elongation complexes. Interestingly, it was observed that in a T7 ternary transcriptional complex arrested by a psoralen cross-link, the nascent RNA transcript could be stabilized from release by the presence in trans of a plasmid DNA bearing a T7 promoter and a T7 terminator. Such a stabilization against RNA release was not observed with plasmid DNAs containing either only a promoter or a terminator. The elongation complexes were stable during gel filtration through Sephacryl S-300 HR. However, it was found that 30% to 45% of the labeled RNA was retained during gel filtration as RNA that was apparently free from ternary complexes.

Abortive initiation by bacteriophage T3 and T7 RNA polymerases under conditions of limiting substrate

Initiation of RNA synthesis by the phage polymerases is abortive if the concentration of pyrimidine triphosphates is limiting. Under abortive initiation conditions the polymerases repeatedly initiate transcription but produce ribooligonucleotides that terminate just prior to the first occurrence of the limiting substrate. Abortive initiation is most severe if the limiting substrate occurs within the first 8-12 nucleotides of the nascent RNA chain and is particularly evident when UMP is limiting. The formation of stable elongation complexes (as determined by gel retardation experiments) occurs after the synthesis of an RNA product 8-12 nucleotides in length.

On the mechanism of rifampicin inhibition of DNA dependent RNA polymerase from Escherichia coli: A new hypothesis of the drug action

The influence of rifampicin on the temperature dependent synthesis of trinucleotides ApUpA and UpApU was studied. Whereas the elongation of dinucleotide ApU is stimulated to a great extent, the elongation of UpA is inhibited to about 50%. These results cannot be explained in terms of different models proposed for the mechanism of inhibition of RNA synthesis caused by rifampicin. According to our hypothesis rifampicin inhibits internal rearrangement of the RNA polymerase which occurs during the transition of the initiation complex to the stable elongation complex.