Central role of Fhl1 and Ifh1 in the synthesis of yeast ribosomal proteins

Abstract

The 138 genes encoding the 79 ribosomal proteins (RPs) of Saccharomyces cerevisiae form the tightest cluster of coordinately regulated genes in nearly all transcriptome experiments. The basis for this observation remains unknown. We now provide evidence that two factors, Fhl1 and Ifh1, are key players in the transcription of RP genes. Both are found at transcribing RP genes in vivo. FHL1 and IFH1 interact genetically. Both proteins are found at transcribing RP genes in vivo. Fhl1 and Rap1, a factor that has been previously implicated in RP gene transcription, constitutively occupy RP gene promoters independent of their transcriptional state. On the contrary Ifh1, which we have demonstrated to be a key regulator of RP genes, leaves the RP promoters when transcription is repressed by inhibiting the target of rapamycin (TOR) pathway. The occupancy of the RP genes by Ifh1 depends on its interaction with the phosphopeptide recognizing Forkhead-Associated (FHA) domain of Fhl1. Disruption of this interaction is severely deleterious to ribosome synthesis and to cell growth. Loss of functional Fhl1 leads to cells that have only 20% the normal amount of RNA and that synthesize ribosomes at only 5--10% the normal rate.;Interestingly, Ifh1 is found as a complex with several other proteins. Two of these namely Utp22 and Rrp7 are involved in the processing of rRNA. In addition, mass spectrometric analysis also revealed the presence of subunits of the kinase CKII (casein kinase II), which has many substrates but has recently been implicated in the activation of transcription. We named this complex the CURI complex (C&barbelow;kII-U&barbelow;tp22-R&barbelow;rp7-I&barbelow;fh1). ChIP analysis revealed that all the components of the CURI complex are present on RP gene promoters. Interestingly, starving yeast cells for Utp22 and Rrp7 results in specific, and considerable increase in RP mRNA levels within the cell, suggesting a repressive role of these proteins. Since the parallel regulation of rRNA and RP synthesis is well established, it is tempting to speculate that this complex serves as a bridge between the two.