RNA polymerase II subunit Rpb9 regulates transcription elongation in vivo

RNA polymerase II lacking the Rpb9 subunit uses alternate transcription ini tiation sites in vitro and in vivo and is unable to respond to the transcri ption elongation factor TFIIS in vitro. Here, we show that RPB9 has a synth etic phenotype with the TFIIS gene. Disruption of RPB9 in yeast also result ed in sensitivity to 6-azauracil, which is a phenotype linked to defects in transcription elongation. Expression of the TFIIS gene on a high-copy plas mid partially suppressed the 6-azauracil sensitivity of Delta rpb9 cells. W e set out to determine the relevant cellular role of yeast RpbS by assessin g the ability of 20 different site-directed and deletion mutants of RPB9 to complement the initiation and elongation defects of Delta rpb9 cells in vi vo. RpbS is composed of two zinc ribbons.' The N-terminal zinc ribbon resto red the wild-type pattern of initiation start sites, but was unable to comp lement the growth defects associated with defects in elongation. Most of th e site-directed mutants complemented the elongation-specific growth phenoty pes and reconstituted the normal pattern of transcription initiation: sites . The anti-correlation between the growth defects of cells disrupted for RP B9 and the selection of transcription:start sites suggests that this is not the primary cellular role for RpbS. Genome-wide transcription profiling of Delta rpb9 cells revealed only a few changes, predominantly in genes relat ed to metabolism.