In Exponentially Growing Saccharomyces cerevisiae Cells, rRNA Synthesis Is Determined by the Summed RNA Polymerase I Loading Rate Rather than by the Number of Active Genes

Abstract

Genes encoding rRNA are multicopy and thus could be regulated by changing the number of active genes or by changing the transcription rate per gene. We tested the hypothesis that the number of open genes is limiting rRNA synthesis by using an electron microscopy method that allows direct counting of the number of active genes per nucleolus and the number of polymerases per active gene. Two strains of Saccharomyces cerevisiae were analyzed during exponential growth: a control strain with a typical number of rRNA genes (∼143 in this case) and a strain in which the rRNA gene number was reduced to ∼42 but which grows as well as controls. In control strains, somewhat more than half of the genes were active and the mean number of polymerases/gene was ∼50 ± 20. In the 42-copy strain, all rRNA genes were active with a mean number of 100 ± 29 polymerases/gene. Thus, an equivalent number of polymerases was active per nucleolus in the two strains, though the number of active genes varied by twofold, showing that overall initiation rate, and not the number of active genes, determines rRNA transcription rate during exponential growth in yeast. Results also allow an estimate of elongation rate of ∼60 nucleotides/s for yeast Pol I and a reinitiation rate of less than 1 s on the most heavily transcribed genes.

ACKNOWLEDGMENTS

This work was supported by Public Health Service grants GM63952 (to A.L.B.) and GM35949 (to M.N.) and by the Human Frontier Science Program Organization (HFSPO) grant RG0336 (to M.N.).

We thank Jeff Smith and Takehiko Kobayashi for strains; Melanie Oakes, David Auble, Tom Misteli, Marisol Santisteban, and Paul Adler for discussion and critical reading of the manuscript; and Martha Sikes and Kristilyn Eliason for excellent technical assistance.