Purification and Characterization of the Simian Virus 40 Transcription Elongation Complex

DNA bending in transcription initiation

Electrophoretic mobility shift (bandshift) phasing analysis and rotational variant topological analysis were performed on initiation complexes formed on the bacteriophage lambda PR promoter. Both the open complex and an abortive complex containing a short RNA primer extending to +3 were characterized. The two methods were used to analyze a series of constructs containing tandemly repeated copies of the PR promoter, with the repeat length increased in single base pair increments to progressively change the rotational setting of adjacent copies. The phasing effect observed in bandshift analysis of open complexes formed on this set of constructs provided qualitative evidence for the presence of a bend. Subsequent rotational variant topological analysis confirmed this and quantified the overall bend angle in the open complex as well as in the +3 abortive complex: a bend of 49 degrees +/- 7 degrees was measured for the open complex, while a bend of 47 degrees +/- 11 degrees was measured for the +3 complex, i.e., the two bends are the same. However, the topological results are not consistent with extensive superhelical wrapping of DNA on either complex as has been proposed. The two complexes do differ in the size of the transcription bubble: the open complex contains a 10.4 +/- 0.1 bp bubble, while that of the +3 complex is 12.2 +/- 0.1 bp, a result consistent with "DNA scrunching" during the onset of transcription. A model for the overall path of the DNA in the open complex is presented that is consistent with the measured bend angle. Measurement of both bubble size and overall bend angle complements the results of crystal structures in providing an enhanced description of the solution structures of the intact initiation complexes.

DNA bubble formation in transcription initiation

The properties of the DNA bubble in the transcription open complex have been characterized by topological analysis of DNA circles containing the lac UV5 promoter or the PR promoter from bacteriophage lambda. Topological analysis is particularly well suited to this purpose since it quantifies the changes in DNA duplex geometry caused by bubble formation as well as by superhelical DNA wrapping. The duplex unwinding that results from bubble formation is detected as a reduction in topological linking number of the DNA circle, and the precision of this measurement has been enhanced in the current study through the use of 8 or 10 promoter copies per circle. Several lines of evidence indicate that the linking number change induced by open complex formation is essentially all due to bubble generation, with very little derived from superhelical wrapping. Accordingly, the linking number change of -1.17 measured for the lac UV5 promoter indicates that the size of the lac UV5 bubble is about 12.3 base pairs, while the change of -0.98 measured for the lambda PR promoter indicates that the lambda PR bubble is 10.3 base pairs. It was also found that the presence or absence of magnesium ion had little effect on the value of the linking number change, a result that resolves the uncertainty associated with use of chemical probes to study the effect of magnesium on bubble size. Finally, the magnitude of linking number change increases progressively when the 3' end of a transcript is extended to +2 and +3 in an abortive initiation complex. This indicates that the transcription bubble expands at its leading edge in the abortive complex, results that confirm and extend the proposal of a DNA "scrunching" mechanism at the onset of transcription. These results are relevant to several models for the structure of DNA in the functional open complex in solution, and provide an important complement to the structural information available from recent crystal structures.

Topological analysis of plasmid chromatin from yeast and mammalian cells

Yeast has proven to be a powerful system for investigation of chromatin structure. However, the extent to which yeast chromatin can serve as a model for mammalian chromatin is limited by the significant number of differences that have been reported. To further investigate the structural relationship between the two chromatins, we have performed a DNA topological analysis of pRSSVO, a 5889 base-pair plasmid that can replicate in either yeast or mammalian cells. When grown in mammalian cells, pRSSVO contains an average of 33 negative supercoils, consistent with one nucleosome per 181 bp. This is close to the measured nucleosome repeat length of 190 bp. However, when grown in yeast cells, pRSSVO contains an average of only 23 negative supercoils, which is indicative of only one nucleosome per 256 bp. This is dramatically different from the measured nucleosome repeat length of 165 bp. To account for these observations, we suggest that yeast chromatin is composed of relatively short ordered arrays of nucleosomes with a repeat of 165 bp, separated by substantial gaps, possibly corresponding to regulatory regions.