RPB9 is a nonessential subunit that has a protein mass of 14kDa. In order to determine cell viability in the absence of RPB9, the gene was replaced with the yeast nutritional marker HIS3. As a result, analysis of the sporulated products demonstrated the regeneration of haploid cells (Woychik 1991). Experiments have been performed to test the temperature dependence of the subunit to enzyme function. Cells lacking the gene grew normally at moderate temperatures (30-33ºC) but failed to grow at hot or cold temperatures (12ºC and 38ºC). Therefore, like RPB4, this subunit plays an important role in maximizing polymerase function at temperature extremes (Woychik 1991).
Deletion of the gene maintains normal levels of transcription, but alteration of the start site selection pattern. An experiment performed in 1995 by Woychik and colleagues demonstrates that loss of RPB9 "does not drastically decrease the level of transcription in vitro." However, the transcripts produced were longer in length than that of the wild type. Therefore this subunit must play a critical role in accurate start site selection (Woychik 1995). Transcription is actually initiated farther upstream in the absence of RPB9 (Woychik 1995).
Another important characteristic of RPB9 is its two metal binding domains and comigration with another subunit. They are cysteine repeat motifs CX2CX18CX2C and CX2CX24CX2C (Woychik 1991). These zinc-finger binding domains span half of the protein. RPB9 comigrates with RPB11 on SDS-polyacrylamide gel. Kornberg and colleagues were able to identify the subunit by performing a multi-step purification that revealed all 12 subunits, as opposed to Young's single step purification that only revealed 10 subunits (Weaver 1999).