Yeasts are fast-growing cells that invest a substantial amount of metabolic energy in ribosome biogenesis and may therefore need to precisely adjust the synthesis of rRNAs, tRNAs, and ribosomal proteins as a function of the growth rate. This regulation is fairly well understood as far as ribosomal proteins are concerned (38
), but comparatively little is known of the control of tRNA and rRNA synthesis. In particular, the extent to which yeast RNA polymerases I and III are coregulated relative to each other and to the transcriptional synthesis of ribosomal proteins is still a moot point. In fact, the main evidence for coordinated control of the transcriptional synthesis of rRNA, ribosomal protein mRNAs, and tRNAs is that blocking protein secretion inhibits these three processes in a way that requires protein kinase C (19
). On the other hand, rRNA and tRNA synthesis can be uncoupled under physiological conditions, such as amino acid starvation (6
). Even under balanced growth conditions, the cellular levels of tRNAs and rRNAs are roughly but not strictly constant, since rRNAs are more strongly affected than tRNAs in slow-growing cells (15
). Finally, conditional mutants of RNA polymerase I or III have no effect on the transcription of ribosomal protein genes by RNA polymerase II (reference 41
and this study), showing that there is no obligatory link between the transcriptional synthesis of rRNA and of ribosomal protein mRNAs.
We show here that RNA polymerase III mutants turn off the formation of the three large rRNA species (25S, 18S, and 5.8S) in parallel to the reduced rate of tRNA synthesis, thereby adapting the flux of newly synthesized rRNA to the low level of tRNA synthesis and keeping the rRNA/tRNA steady-state ratio at the wild-type level. An obvious concern is that this could somehow be the indirect result of a common dependency on growth rate. The fast response of rpc160-112
cells when shifted to 37°C argues against this interpretation, since they reach a low rate of rRNA synthesis within one doubling time, well before growth arrest is observed. This coordinated synthesis of tRNAs and rRNAs could partly involve transcriptional effects, as in secretion-defective cells (19
), and may perhaps also reflect changes in RNA turnover. However, our data strongly suggest an additional effect on pre-RNA processing, as shown by the increase of 20S pre-rRNA observed in the rpc160-112
mutants. This is consistent with previous data showing that RNA polymerase III mutants grown at 30°C have minor but distinct effects on pre-rRNA processing (13
). Conversely, we also observed that RNA polymerase I mutant cells accumulate a high level of pre-tRNALeu3
and thus probably interfere with tRNA processing.
The mechanism by which RNA polymerase III may control pre-rRNA processing is unknown. One possibility is that a hypothetical RNA polymerase III holoenzyme (5
) may contain or contact nucleolar proteins participating in pre-rRNA processing. This could arguably account for the allele-specific differences in the rRNA processing defects of the rpc160-112
mutants at 25°C, as these mutants are thought to have a different effect on the conformation of the elongating RNA polymerase III complex (34
). Alternatively, RNA polymerase III transcripts could directly participate in pre-rRNA processing. This is the case for U3 snRNA in plants (16
) or RNase MRP RNA in mammals (43
), but the yeast counterparts are made by RNA polymerase II (reference 14
and this work). RNase P RNA is another candidate, as it affects 5.8S rRNA maturation in vivo (4
) and is an RNA polymerase III transcript in organisms ranging from yeasts (17
) to humans (2
). Moreover, its high dosage partly suppresses a mutant defective in the RNA polymerase III initiation factor TFIIIC (18
). Finally, yeast 5S rRNA mutants interfere with pre-rRNA processing, providing another link to RNA polymerase III (7
). Native 5S rRNA is short-lived (probably reflecting its lack of nucleotide modification) (33
) unless it is complexed by yeast ribosomal protein L1 (8
). It could therefore operate as a sensor, stimulating pre-rRNA processing in response to RNA polymerase III activity. Unlike RNA polymerase III mutants, however, 5S rRNA mutants mainly interfere with 25S rRNA maturation, with little effect on 18S rRNA (7
) (Fig. ).
In human cells, transcriptional controls over tRNA and rRNA synthesis are probably critical to the (de)regulation of differentiated cell growth upon viral infection or tumorigenesis, as shown by the inhibitory effect of the retinoblastoma and p53 tumor-suppressing factors on RNA polymerases I and III (reference 39
and references therein). Our observation that yeast cells adjust pre-rRNA processing as a function of RNA polymerase III activity extends the repertoire of homeostatic controls of ribosome synthesis (21
). It would be interesting to know if a similar situation exists in human cells. Moreover, U6 snRNA and the signal recognition particle RNA are made by RNA polymerase III in organisms ranging from yeasts to humans, thus relating RNA polymerase III activity to mRNA splicing and cotranslational protein secretion. Taken together, these data underscore the highly pleiotropic role of RNA polymerase III in modulating the main steps of RNA and protein synthesis.