Transcriptional elements involved in the repression of ribosomal protein synthesis

The ribosomal proteins (RPs) of Saccharomyces cerevisiae are encoded by 137 genes that are among the most transcriptionally active in the genome. Thes e genes are coordinately regulated: a shift up in temperature leads to a ra pid, but temporary, decline in RP mRNA levels. A defect in any part of the secretory pathway leads to greatly reduced ribosome synthesis, including th e rapid loss of RP mRNA. Here we demonstrate that the loss of RP mRNA is du e to the rapid transcriptional silencing of the RP genes, coupled to the na turally short lifetime of their transcripts. The data suggest further that a global inhibition of polymerase II transcription leads to overestimates o f the stability of individual mRNAs. The transcription of most RP genes is activated by two Rap1p binding sites, 250 to 400 bp upstream from the initi ation of transcription. Rap1p is both an activator and a silencer of transc ription. The swapping of promoters between RPL30 and ACT1 or GAL1 demonstra ted that the Rap1p binding sites of RPL30 are sufficient to silence the tra nscription of ACT1 in response to a defect in the secretory pathway. Sir3p and Sir4p, implicated in the Rap1p-mediated repression of silent mating typ e genes and of telomere-proximal genes, do not influence such silencing of RP genes. Sir2p, implicated in the silencing both of the silent mating type genes and of genes within the ribosomal DNA locus, does not influence the repression of either RP or rRNA genes. Surprisingly, the 180-bp sequence of RPL30 that lies between the Rap1p sites and the transcription initiation s ite is also sufficient to silence the Gal4p-driven transcription in respons e to a defect in the secretory pathway, by a mechanism that requires the si lencing region of Rap1p. We conclude that for Rap1p to activate the transcr iption of an RP gene it must bind to upstream sequences; yet for Rap1p to r epress the transcription of an RP gene it need not bind to the gene directl y. Thus, the cell has evolved a two-pronged approach to effect the rapid ex tinction of RP synthesis in response to the stress imposed by a heat shock or by a failure of the secretory pathway. Calculations based on recent tran scriptome data and on the half-life of the RP mRNAs suggest that in a rapid ly growing cell the transcription of RP mRNAs accounts for nearly 50% of th e total transcriptional events initiated by RNA polymerase II. Thus, the su dden silencing of the RP genes must have a dramatic effect on the overall t ranscriptional economy of the cell.