RNA polymerase (RNA pol) subunit composition.
RNA polymerases are heteromultimeric complexes responsible of RNA synthesis. In yeast, as in the other eukaryotes, these complexes contain five common subunits (Rpb5, Rpb6, Rpb8, Rpb10 and Rpb12) that must have similar functions in the three RNA polymerases. However, some of these proteins have been shown to also have specific roles. In the last few decades, substantial progress has been made to understand the role of these common subunits in transcription, but their participation in the activity of each enzyme remains unclear. This review gives a comprehensive overview of current knowledge on the five common subunits of eukaryotic RNA pol, placing attention not only on their common roles in the activity of the RNA pols but also on describing specific roles for some of the complexes.
- RNA polymerases
- protein complexes
- common subunits
Transcription is carried out by the RNA polymerases (RNA pol). While archaea and bacteria contain only one RNA pol, most eukarya contain three different enzymes responsible for the specific synthesis of different types of RNAs . RNA pol I synthesises the precursor of the three largest rRNAs, whereas RNA pol III sy\nthesises mostly tRNAs and 5S rRNA, together with several short non-translated RNAs. Meanwhile, RNA pol II produces all mRNAs and many non-coding RNAs [1, 2]. Moreover, in plants, two additional polymerases, IV and V (or nuclear RNA polymerases D and E), reportedly synthesise small interfering RNAs (siRNAs), regulating methylation and participating in gene silencing, as well as long non-coding RNAs involved in development and response to environmental changes [3, 4, 5].
While bacteriophage T7 and some related enzymes that transcribe the mitochondrial genome or contribute to chloroplast transcription are single-subunit RNA polymerase , bacterial, archaeal and eukaryotic enzymes are heteromultimeric complexes (Table 1). As in other eukaryotes, yeast RNA pol I, II and III are composed of 14, 12 and 17 subunits, respectively. These contain a catalytic core formed by the two largest subunits, which are highly conserved through evolution (Rpb1 and Rpb2). Moreover, among all eukaryotic RNA pol subunits, five have bacterial homologues (Rpb1, Rpb2, Rpb3, Rpb6 and Rpb11) and others are common to archaea, but without bacterial homologues (Rpb4, Rpb5, Rpb7, Rpb8, Rpb9, Rpb10, and Rpb12) [1, 2, 6, 7, 8, 9]. Finally, eukaryotic RNA pols contain five common subunits to the three enzymes (Rpb5, rpb6, Rpb8, Rpb10 and Rpb12), which have archaeal homologues (Figure 1) [10, 11, 12].
|Bacteria||Archaea||RNA pol I||RNA pol II||RNA pol III||RNA pol IV (plants)||RNA pol V (plants)|
|α||Rpo3 (RpoD)||RPAC40||RPB3||RPAC40||RPB3 ||RPB3 |
|ω||Rpo6 (RpoK)||RPB6||RPB6||RPB6||RPB6 ||RPB6|
|Rpo5 (RpoH)||RPB5||RPB5||RPB5||RPB5 ||NRPES5|
|Rpb8 (RpoG)*||RPB8||RPB8||RPB8||RPB8 ||RPB8 |
In the last few decades, substantial progress has been made to understand the role of the RNA pol common subunits in transcription, but their participation in the activity of each enzyme remains unclear. This review gives a comprehensive overview of current knowledge on the five common subunits of eukaryotic RNA pol, placing attention not only on their common roles in the activity of the RNA pols but also on describing specific roles for some of the complexes.
In budding yeast, the essential Rpb5 subunit, also known as ABC27, consists of 215 amino acid residues and has a molecular mass of 27 kDa [11, 13, 14, 15]. Contrary to other RNA polymerase common subunits, human Rpb5 homologue (RPB5), with 44% identity and 80% similarity to the yeast polypeptide, fails to complement the
Structurally, Rpb5 has a bipartite organisation combining two globular modules separated by a short hinge: an N-terminal domain (“
The periphery localization of Rpb5 on all three enzymes [7, 30, 31] would allow possible interactions with general transcription factors or specific gene regulators. It should be the basis of the interaction between Rpb5 and Rsc4, a subunit of RSC (chromatin remodeler complex) in
The HBx transactivation seems to be modulated by the protein URI/RMP (Unconventional Prefoldin Rpb5 Interactor) that specifically binds to RPB5 both
Furthermore, it has been proposed that Bud27 modulates the association between Sth1 (subunit of RSC complex) and the RNA pol II probably through Rpb5 interaction in
Rpb6 (also known as ABC23 or Rpo26) is an acidic 155-amino acid subunit with apparent and predicted molecular masses of 23 and 18 kDa, respectively [11, 47]. It is phosphorylated in all three RNA pols, mainly on serine and threonine residues [48, 49, 50, 51]. Moreover, the
A role for Rpb6 in transcription elongation has been proposed. In fact, some temperature-sensitive mutants in
According to a global role of Rpb6 in transcription, the
Rpb6 was found to make contact with three small RNA pol subunits, Rpb5, Rpb7 and Rpb8, as well as with the foot of the RNA pol II, with its largest subunits Rpb1 and Rpb2 [7, 61]. Similarly, Rpb6 interacts on the crystal structure with the largest subunit of the RNA pol I, Rpa190  and probably with its homologue in the RNA pol III, Rpc160. Notably, the contact between Rpb6 and Rpb7 involves the residue Gln100 of Rpb6 and Gly66 of Rpb7 on the RNA pol II core and the
While the C-terminal segment of Rpb6, from amino acids 72 to 155, is well organised on the crystal structure of yeast RNA pol II , the N-terminal domain 71-amino acid segment on the RNA pol II structure, as well as the N-terminal 54-amino acid segment on the RNA pol I structure is disordered [24, 28, 30]. Moreover, the segment from amino acids 55 to 71 of Rpb6 on the RNA pol I structure comprises an α-helix that provides additional contacts with Rpa43 and Rpa14 [28, 30]. The N-terminal region of Rpb6 seems to be dispensable for the functions of this subunit, explaining the lack of conservation of this region with its archaeal homologues and the low degree of similarity of the Rpb6 sequence among various eukaryotes . However, a region of 13 amino acids in the C-terminal domain of Rpb6 is highly conserved in eukaryotes and archaea, suggesting an essential function . Rpb6 is connected to the base of a flexible module containing portions of Rpb1 and Rpb2, called the clamp, through a set of five “switches” that control clamp movement . In addition, the association of Rpb6 with Rpb4/Rpb7 dimmer suggest that these two subunits could modulate the clamp movement and may regulate the position of the clamp by signalling through Rpb6 .
Rpb6 and its bacterial homologue have been proposed to promote RNA pol II assembly and/or increase RNA pol stability, through specific interactions with the RNA pol II largest subunit, Rpb1, in the case of
Rpb8 (also known as ABC14.5) is an essential subunit of 16.5 kDa conserved among eukaryotes and thought to be restricted to them [11, 12, 67]. However, recently, the Rpb8 archaeal orthologues, called G or Rpo8, has been identified in
Rpb8 crystal structure in RNA pol II contains nine closely packed β-strands forming a double OB-fold . Rpb8 interacts with the largest subunit of the RNA pol II, Rpb1, and shows a subunit interface between Rpb3 and Rpb11. Two-hybrid analyses identified similar binding of Rpb8 to the Rpb1-like subunits of RNA pol I (Rpa190) and RNA pol III (Rpc160) . In addition, mutational analysis of
As opposed to the Rpb8 human orthologue,
Rpb10, also called AB10β in yeast, is one of the smallest polypeptides (70-aminoacid polypeptide in
All the eukaryotic forms of Rpb10 share an invariant HVDLIEK motif (located between positions His-53 and Pro-65 in
Rpb10 is localised in the periphery of all three RNA polymerases [7, 30, 31]. In budding yeast, Rpb10 was described to interact not only with two essential subunits of the RNA pols I and III, Rpac40 and Rpac19 (homologous to Rpb3 and Rpb11, respectively, in the RNA pol II) but also with the two largest subunits of RNA pol I (Rpa190 and Rpa135) and their homologues in RNA pol III (Rpc160 and Rpc128) [23, 72].
Rpb10 has been found to be involved in the assembly of RNA polymerases in eukaryotes as part of the assembly platform. In fact, it has been proposed that Rpb10 and Rpb12 form a stable complex with Rpb3-Rpb11 (homologous to the bacterial α-subunit homodimer) . Rpb10 and Rpb12 fill concave depressions of Rpb2 and thereby act as structural adaptors between Rpb2 and Rpb3 (reviewed in ). Notably, mutations of the invariant HVDLIEK motif lead to a complete depletion of the largest RNA pol I subunit (Rpa190) and decrease the accumulation of mature rRNA species transcribed by RNA pol I . However, Rpb10 could have additional functions beyond RNA polymerases assembly. In accordance, Rpb10 is localised in proximity to TBP in the structural model of the DNA-TBP-TFIIB-RNA pol II transcription initiation complex .
The eukaryotic subunit Rpb12, also designated as ABC10α [71, 80], together with Rpb10 are the smallest common subunits to the RNA pols. The corresponding gene is essential for growth in
The importance of Rpb12 in transcription is extrapolated from studies on the archaeal P subunit. The P subunit is involved in promoter opening. The ΔP enzyme is unable to form stable open complexes and its activity can be rescued by the addition of Rpb12 or subunit P to transcription reactions. Notably, mutation of cysteine residues in the zinc ribbon impairs the activity of the enzyme in transcription reactions. The conserved zinc ribbon in the N-terminus seems to be important for proper interaction of the complete subunit with other RNA polymerase subunits, and a 17-amino acid C-terminal peptide is sufficient to support all basic RNA polymerase functions
The contact between
This work has been supported by grants from the Spanish Ministry of Economy and Competitiveness, MINECO, and FEDER funds (BFU2013-48643-C3-2-P and BFU2016-77728-C3-2-P to F.N.) and Junta de Andalucía (BIO258).
A.C.B. was a recipient of a FPI predoctoral contract from MINECO. V.M.F. was recipient of a fellowship from Junta de Andalucía and a postdoctoral fellowship from the Junta de Andalucía-University of Jaén. A.I.G-G was a recipient of MEC and a postdoctoral fellowship from the University of Jaén.