Specific Features of RNA Polymerases I and III: Structure and Assembly

Abstract

RNA polymerase I (RNAPI) and RNAPIII are multi-heterogenic protein complexes that specialize in the transcription of highly abundant non-coding RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA). In terms of subunit number and structure, RNAPI and RNAPIII are more complex than RNAPII that synthesizes thousands of different mRNAs. Specific subunits of the yeast RNAPI and RNAPIII form associated subcomplexes that are related to parts of the RNAPII initiation factors. Prior to their delivery to the nucleus where they function, RNAP complexes are assembled at least partially in the cytoplasm. Yeast RNAPI and RNAPIII share heterodimer Rpc40-Rpc19, a functional equivalent to the αα homodimer which initiates assembly of prokaryotic RNAP. In the process of yeast RNAPI and RNAPIII biogenesis, Rpc40 and Rpc19 form the assembly platform together with two small, bona fide eukaryotic subunits, Rpb10 and Rpb12. We propose that this assembly platform is co-translationally seeded while the Rpb10 subunit is synthesized by cytoplasmic ribosome machinery. The translation of Rpb10 is stimulated by Rbs1 protein, which binds to the 3'-untranslated region of RPB10 mRNA and hypothetically brings together Rpc19 and Rpc40 subunits to form the αα-like heterodimer. We suggest that such a co-translational mechanism is involved in the assembly of RNAPI and RNAPIII complexes.

Keywords: RNA polymerase I; RNA polymerase III; complex assembly; rRNA; tRNA; transcription factors.

FIGURE 1

Comparison of RNAPI and RNAPIII structures and transcription factors. (A) General architecture of RNAPII, consisting of the catalytic core and stalk. RNAPII core consists of a DNA binding channel, catalytic center, and assembly platform. RNAPII binds multiple transcription factors (TFs). Some TFs are homologous to additional subunits of specialized RNAPs (i.e., TFIIF). (B) Subunit composition of eukaryotic RNAPs. Human nomenclature is shown for comparision. Please note that C-terminal region of Rpa49 subunit harbors a “tandem winged helix” which is predicted in TFIIE and that human RNAPIII RPC7 subunit is coded by two isoforms α and β. The question mark indicates name unconfirmed. (C) Subunit composition of yeast RNAPI. (D) Model of the RNAPI pre-initiation complex, showing an early intermediate with visible Rrn3 and core factor (CF). TATA-binding protein (TBP) and upstream-associated factor (UAF) are added schematically. (E) Subunit composition of yeast RNAPIII. (F) Atomic model of RNAPIII pre-initiation complex with TFIIIB. The Rpc82/34/31 heterotrimer is involved in initiation and marked in green as in E. TFIIIC is added schematically. PDB: 5C4X, 5FJ8, 4C3J, 6EU0, and 6TPS (Fernández-Tornero et al., 2013; Barnes et al., 2015; Hoffmann et al., 2015; Abascal-Palacios et al., 2018; Pilsl and Engel, 2020).

FIGURE 2

Model of RNAPIII biogenesis in the yeast Saccharomyces cerevisiae. The control of Rpb10 expression and role of Rpb10 in assembly of the RNAP III complex are connected via a regulatory loop that involves Rbs1 protein. Possible ways in which subunits of the RNAPIII intermediate complex are brought together for co-translational assembly are shown. The initial step of RNAPIII assembly in Saccharomyces cerevisiae occurs in the cytoplasm. Formation of the intermediate Rpc128-Rpc40-Rpc19-Rpb12-Rpb10 subcomplex is seeded co-translationally while the Rpb10 subunit is being synthesized by cytoplasmic ribosomes. Rbs1 is an RNA binding protein that stimulates the translation of Rpb10 protein through an interaction of the R3H domain with the 3′-UTR in RPB10 mRNA. Rpb10 brings together the Rpc19 and Rpc40 subunits to form the α-like heterodimer. One possibility is that Rbs1 binds and recruits the mature Rpc40 subunit to the 3′-UTR of RPB10 mRNA, which undergoes translation. The Rpc40-Rbs1 interaction has been previously demonstrated by co-immunoprecipitation. Alternatively, Rbs1 protein directly bridges RPB10 mRNA and RPC19 mRNA. A fully folded subunit that formed on one mRNA was recently shown to detach from its ribosome and interact with a nascent protein on another mRNA (Cieśla et al., 2015, 2020).