The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications

Abstract

Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription preinitiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.

Regulation of Eukaryotic RNAPs Activities by Phosphorylation

“…A sophisticated network of protein-protein and protein-nucleic acid interactions is established, producing conformational and activity changes in RNAPII through the transcription cycle. Thus, a pre-initiation complex (PIC), composed basically of general transcription factors (GTFs: TFIIA, B, D, E, F, and H), Mediator and RNAPII, is assembled at the gene promoters, opening the DNA to initiate transcription (Greber and Nogales, 2019;Schier and Taatjes, 2020). Other factors acting as activators/co-activators and repressors/co-repressors can modulate the transcription activity (Ho and Shuman, 1999;Thomas and Chiang, 2006;Hahn and Young, 2011;Roeder, 2019).…”

“…Functional and structural studies with S. cerevisiae have provided the majority of the existing knowledge about RNAPII transcription mechanisms, regulation and coordination with other cellular processes (Cramer, 2019a;Cramer, 2019b;Roeder, 2019). Recent structural data combined with functional studies have advanced our understanding of RNAPII transcription in general and that of PIC function, structure and dynamics in particular (Greber and Nogales, 2019;Schier and Taatjes, 2020). Resolution of the RNAPII structure by X-ray crystallography about 20 years ago showed that its twelve subunits are folded and assembled into four mobile modules: the core module, formed by the active center (Rpb1 and Rpb2) and assembly platform (Rpb3, Rpb10, Rpb11, and Rpb12); the jaw-lobe module, made up of Rpb1 and Rpb9; the shelf module containing the foot and cleft domains of Rpb1 and the lower jaw and assembly domains of Rpb5; and the stalk module, formed by Rpb4 and Rpb7, which in the case of S. cerevisiae can be dissociated from the 10-subunit core polymerase (Cramer et al, 2000;Cramer et al, 2001;Gnatt et al, 2001;Armache et al, 2003;Bushnell and Kornberg, 2003).…”

“…Subsequent binding of elongation factors replaces the GTFs, thus regulating further steps of the transcription cycle. How all these events take place is not fully understood, although some are explained by conformational changes of the transcription complex and/or phosphorylation of specific factors and the Rpb1-CTD (Wang et al, 2010;Larochelle et al, 2012;He et al, 2013;Sainsbury et al, 2015;He et al, 2016;Harlen and Churchman, 2017;Nogales et al, 2017;Greber and Nogales, 2019;Nogales and Greber, 2019;Patel et al, 2019;Schier and Taatjes, 2020).…”

“…Thus, it is tempting to speculate that the phosphorylation of these residues might be important for protein-protein interaction between RNAPII and different transcriptional regulators. In fact, these exposed residues localize in regions that are described to contact the GTFs (TFIIB, TBP, TFIIA, TFIIE, TFIIF, TFIIH or TFIIS; Figure 1B), Mediator and elongation factor Spt5/4 (Cai et al, 2010;Martinez-Rucobo et al, 2011;Nogales et al, 2017;Greber and Nogales, 2019;Schier and Taatjes, 2020). Interestingly, there are three phospho-sites (S1793, T1471, and Y1473) within the Rpb1 linker, an unstructured region that connects the CTD to the rest of the protein, whose phosphorylation is required for Spt6 interaction with RNAPII and the re-assembly of repressive chromatin during transcription (Sdano et al, 2017).…”

Enzymatic Protein Biopolymers as a Tool to Synthetize Eukaryotic Messenger Ribonucleic Acid (mRNA) with Uses in Vaccination, Immunotherapy and Nanotechnology

“…This PIC is a large protein biopolymer with a molecular weight of about 3 M Da [ 1 ]. During the last decade, the X-ray crystallographic structures of several PICs containing different arrangement of RNAPII, TFIIs (GTFs) and coactivators have been solved and they are reviewed in reference [ 9 ].…”