Does Pol I talk to Pol II? Coordination of RNA polymerases in ribosome biogenesis: Figure 1.

Abstract

To grow and to divide, cells are dependent on protein synthesis, and protein synthesis depends on ribosomes. Ribosomes are complex molecular machines that contain four different RNA molecules and 79 different proteins, produced by three different RNA polymerases. RNA polymerase I (Pol I) synthesizes the large ribosomal RNA (rRNA) precursor (35S RNA in yeast), which is then processed into mature 18S, 28S, and 5.8S RNAs; RNA polymerase II (Pol II) synthesizes the mRNAs encoding the ribosomal proteins; and RNA polymerase III (Pol III) synthesizes the small 5S RNA molecule. The biosynthesis of ribosomes by the three RNA polymerases uses an enormous amount of the cell resources. In a yeast cell, rRNA transcription represents ∼60% of total transcription, and transcription of the ribosomal protein mRNAs represents ∼50% of all Pol II transcription initiation events (Warner 1999; Rudra and Warner 2004). Accordingly, ribosome biosynthesis is tightly regulated with cell growth and proliferation. Thus, when the demand for protein synthesis is reduced, as occurs with cells in stationary phase after nutrient deprivation, the production of new ribosomes is greatly reduced. Ribosome assembly requires the coordinated production of ribosome components. On the one hand, equimolar amounts of each ribosome protein must be produced. In yeast, the coregulation of ribosomal protein synthesis is exerted mainly at the level of ribosomal protein gene transcription. On the other hand, sufficient amounts of each ribosomal protein must be produced to allow correct assembly and processing of rRNAs. This suggests that the ribosomal protein and rRNA synthesis machineries are somehow coregulated. Indeed, an essential signal transduction pathway for the modulation of rRNA, ribosomal proteins, and 5S rRNA in response to nutrient availability is the TOR (Target of Rapamycin) kinase pathway. This pathway is activated in the presence of nutrients, and inactivation of TOR—for example, by the antibiotic rapamycin—mimics the effects of starvation (for review, see Crespo and Hall 2002). Rapamycin inhibition of the TOR pathway is known to repress rRNA transcription by Pol I, Pol III transcription, and Pol II transcription of ribosomal protein genes (Zaragoza et al. 1998; Powers and Walter 1999). However, we still know little about how TOR controls ribosome component synthesis, in particular, whether each of the three RNA polymerase machineries is controlled separately, whether one of them is the primary target that then controls the others, or whether several mechanisms of crosstalk ensure coordinated regulation. In this issue of Genes & Development, Laferte et al. (2006) present data suggesting that in yeast, accumulation of large ribosomal RNAs as a result of deregulated Pol I transcription leads to a corresponding accumulation of ribosomal proteins, 5S rRNA, and fully assembled ribosomes. Thus, increased Pol I transcription activity can orchestrate the coordinated increased accumulation of all ribosomal components, suggesting a central role for RNA polymerase I activity in the coordination of ribosomal component synthesis. Transcription by Pol I in yeast is known to depend on four factors: Three of them—TBP (TATA-box binding protein) and the multisubunit complexes UAF (upstream activating factor) and CF (core factor)—bind together to rDNA promoters; the fourth, Rrn3, associates reversibly with Pol I and renders it competent for transcription initiation, at least in part by bridging Pol I and the promoter-bound factors (for review, see Moss and Stefanovsky 2002; Grummt 2003; Russell and Zomerdijk 2006). The association of Rrn3 with Pol I controls the activity of the enzyme, and the percentage of active Pol I in the cell appears in turn to play a determinant role in the control of rRNA transcription. The investigators created a yeast strain, which they named CARA (for Constitutive Association of Rrn3 and A43), in which the endogenous genes coding for Rrn3 and A43, the Pol I subunit with which Rrn3 is known to associate (Peyroche et al. 2000), were deleted. Rrn3 and A43 activities were supplied as a fusion protein expressed from a 2-μ plasmid. The fusion protein assembled properly with the other Pol I subunits to form a constitutively active enzyme. Remarkably, under normal growth conditions, the CARA strain behaves like the wild type: It has the same doubling time and the same amount of ribosomal particles, and it has a similar mRNA expression pattern. Thus, the CARA strain has a normal physiology. Modulation of Pol I transcription through TOR targets Rrn3. Upon rapamycin treatment, Rrn3 dissociates from the Pol I complex, resulting in an arrest of transcription Corresponding author. E-MAIL Nouria.Hernandez@unil.ch; FAX 41-21-692-39-25. Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.1460706.