Retention of transcription initiation factor σ70 in transcription elongation:: Single-molecule analysis

We report a single-molecule assay that defines, simultaneously, the translocational position of a protein complex relative to DNA and the subunit stoichiometry of the complex. We applied the assay to define translocational positions and sigma(70) contents of bacterial transcription elongation complexes in vitro. The results confirm ensemble results indicating that a large fraction, similar to 70%-90%, of early elongation complexes retain sigma(70) and that a determinant for sigma(70) recognition in the initial transcribed region increases sigma(70) retention in early elongation complexes. The results establish that a significant fraction, similar to 50%-60%, of mature elongation complexes retain sigma(70) and that a determinant for sigma(70) recognition in the initial transcribed region does not appreciably affect sigma 70 retention in mature elongation complexes. The results further establish that, in mature elongation complexes that retain sigma(70) the half-life of sigma(70) retention is long relative to the timescale of elongation, suggesting that some complexes may retain sigma(70) throughout elongation.