Budding yeast RNA polymerase III (Pol III) contains a small, essential subunit, named C11, that is conserved in humans and shows a strong homology to TFIIS. A mutant Pol III, heterocomplemented with Schizosaccharomyces pombe C11, was affected in transcription termination in vivo. A purified form of the enzyme (Pol III ⌬), deprived of C11 subunit, initiated properly but ignored pause sites and was defective in termination. Remarkably, Pol III ⌬ lacked the intrinsic RNA cleavage activity of complete Pol III. In vitro reconstitution experiments demonstrated that Pol III RNA cleavage activity is mediated by C11. Mutagenesis in C11 of two conserved residues, which are critical for the TFIIS-dependent cleavage activity of Pol II, is lethal. Immunoelectron microscopy data suggested that C11 is localized on the mobile thumb-like stalk of the polymerase. We propose that C11 allows the enzyme to switch between an RNA elongation and RNA cleavage mode and that the essential role of the Pol III RNA cleavage activity is to remove the kinetic barriers to the termination process. The integration of TFIIS function into a specific Pol III subunit may stem from the opposite requirements of Pol III and Pol II in terms of transcript length and termination efficiency.

While initiation of transcription by RNA polymerase III (Pol III) has been thoroughly investigated, molecular mechanisms driving transcription termination remain poorly understood. Here we describe how the characterization of the in vitro transcriptional properties of a Pol III variant (Pol IIIdelta), lacking the C11, C37, and C53 subunits, revealed crucial information about the mechanisms of Pol III termination and reinitiation. The specific requirement for the C37-C53 complex in terminator recognition was determined. This complex was demonstrated to slow down elongation by the enzyme, adding to the evidence implicating the elongation rate as a critical determinant of correct terminator recognition. In addition, the presence of the C37-C53 complex required the simultaneous addition of C11 to Pol IIIdelta for the enzyme to reinitiate after the first round of transcription, thus uncovering a role for polymerase subunits in the facilitated recycling process. Interestingly, we demonstrated that the role of C11 in recycling was independent of its role in RNA cleavage. The data presented allowed us to propose a model of Pol III termination and its links to reinitiation.

Regulation of ribosome biogenesis is a key element of cell biology, not only because ribosomes are directly required for growth, but also because ribosome production monopolizes nearly 80% of the global transcriptional activity in rapidly growing yeast cells. These observations underscore the need for a tight regulation of ribosome synthesis in response to environmental conditions. In eukaryotic cells, ribosome synthesis involves the activities of the three nuclear RNA polymerases (Pol). Although postulated, there is no clear evidence indicating whether the maintenance of an equimolar supply of ribosomal components reflects communication between the nuclear transcriptional machineries. Here, by constructing a yeast strain expressing a Pol I that remains constitutively competent for the initiation of transcription under stress conditions, we demonstrate that derepression of Pol I transcription leads to a derepression of Pol II transcription that is restricted to the genes encoding ribosomal proteins. Furthermore, we show that the level of 5S rRNA, synthesized by Pol III, is deregulated concomitantly with Pol I transcription. Altogether, these results indicate that a partial derepression of Pol I activity drives an abnormal accumulation of all ribosomal components, highlighting the critical role of the regulation of Pol I activity within the control of ribosome biogenesis.[Keywords: Ribosome biogenesis; RNA polymerase I; transcription; yeast] Supplemental material is available at http://www.genesdev.org.

The structure of the yeast RNA polymerase (pol) III was investigated by exhaustive two-hybrid screening using a library of random genomic fragments fused to the Gal4 activation domain. This procedure allowed us to identify contacts between individual polypeptides, localize the contact domains, and deduce a protein-protein interaction map of the multisubunit enzyme. In all but one case, pol III subunits were able to interact in vivo with one or sometimes two partner subunits of the enzyme or with subunits of TFIIIC. Four subunits that are common to pol I, II, and III (ABC27, ABC14.5, ABC10␣, and ABC10␤), two that are common to pol I and III (AC40 and AC19), and one pol III-specific subunit (C11) can associate with defined regions of the two large subunits. These regions overlapped with highly conserved domains. C53, a pol III-specific subunit, interacted with a 37-kDa polypeptide that copurifies with the enzyme and therefore appears to be a unique pol III subunit (C37). Together with parallel interaction studies based on dosagedependent suppression of conditional mutants, our data suggest a model of the pol III preinitiation complex.Eukaryotic transcription is mediated by large multiprotein complexes in which each of the three nuclear RNA polymerases (pols) interact with their cognate preinitiation factors. The pols themselves have been well characterized in terms of subunit composition, especially in the case of the yeast Saccharomyces cerevisiae. However, the spatial organization of the enzyme subunits and the way they interact with preinitiation complexes or with other components of the yeast nucleus are still poorly understood. Electron microscopy so far has provided the most accurate structural description of the Escherichia coli enzyme (1) and of yeast pol I (2, 3) and II (refs. 4-6 and references therein), revealing a striking similarity in the overall shape of these enzymes. In the case of yeast pol I, six subunits (or domains thereof) were localized by immunoelectron microscopy of antibody-labeled enzymes (2, 7). Sitespecific protein-DNA crosslinking also shed light on the general architecture of pol II (8, 9) and III (10-12) transcription complexes.These studies are still far from providing a comprehensive picture of the structural organization of the eukaryotic pols. Alternatively, each subunit can be tested for its ability to selectively associate with other subunits of the same heteromultimeric complex. In the case of human pol II, an in vitro test based on glutathione S-transferase pull-down assays has suggested numerous contacts within the pol II complex (13). In Schizosaccharomyces pombe, studies based on Far Western blotting, which were in some cases supported by independent protein-protein crosslinking studies, suggested that the two large pol II subunits interact with all of the other smaller subunits (9, 14). The two-hybrid system is an alternative to biochemical methods that allows one to detect interactions between proteins in the cellular context of the yeast nucleus (ref. 15 and ...

The AC40 and AC19 subunits (encoded by RPC40 and RPC19) are shared by yeast RNA polymerases I and HI and have a local sequence similarit to prokaryotic a subunits. Mutational analysis of the corresponding "a motif"indicated that its integrity is essential on AC40 subunit but is not essential on AC19 subunit. By applying the two-hybrid method, these two polypeptides were shown to a ate in vivo. (2,(20)(21)(22). The bacterial core enzyme also contains the dimeric a subunit (23) that initiates enzyme assembly (24) and has a C-terminal domain involved in selective interactions with transcriptional regulators (25,26). The B44 dimer of RNA polymerase II (homologous to the AC40 subunit shared by enzymes I and III) has some sequence similarity to a (17, 27). AC19 subunit also shows some local sequence similarity to a, at the level of a putative "a motif' (18). We show here that these two common subunits associate in vivo and interact with the small zinc-binding subunit ABC1O0,,* which is shared by all three RNA polymerases. Mutational analysis showed that the a motives of AC19 and AC40 subunits are not equivalent, the integrity of the motif being essential in growth for AC40 subunit but not essential in growth for AC19 subunit. Mutagenesis. Plasmids p7040 (URA3 RPC40) and p3519 (TRPI RPC)9) were mutagenized (50) on their a motif and checked by determining their DNA sequence over =250 bp around the mutated site. Individual plasmids were introduced in strains DLY11 and DLY200 (see Table 1), respectively, and analyzed by plasmid shuffling (16). DLY11 subclones lacking DLpO1 (TRP) RPC40 SUP))-)) were isolated as red sectors on yeast extract/dextrose/peptone (YPD) medium, reflecting the lack of suppression of the ochre allele ade2-1 in the absence of SUP))-) (37). DLY200 subclones lacking p7519 (URA3 RPCl9) were selected as uracil auxotrophs in the presence of5-fluoroorotic acid (38). Failure to yield these subclones indicated that the mutant rpc4O or rpcl9 allele (borne on p7040 or p3519) was unable to complement the chromosomal null alleles rpc4O-A::HIS3 or rpc)9-A::HIS3. MATERIALS AND METHODS