Structure and function of archaeal RNA polymerases

Abstract

SummaryRNA polymerases (RNAPs) are essential to all life forms and therefore deserve our special attention. The archaeal RNAP is closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. RNAPs of this class are large and sophisticated enzymes that interact in a complex manner with DNA/RNA scaffolds, substrates NTPs and a plethora of transcription factors -interactions that often result in an allosteric regulation of RNAP activity. The 12 subunits of RNAP play distinct roles including RNAP assembly and stability, catalysis and functional contacts with exogenous factors. Due to the availability of structural information of RNAPs at high-resolution and wholly recombinant archaeal transcription systems, we are beginning to understand the molecular mechanisms of archaeal RNAPs and transcription in great detail.

Multisubunit DNA-Dependent RNA Polymerases from Vaccinia Virus and Other Nucleocytoplasmic Large-DNA Viruses: Impressions from the Age of Structure

“…Consistent with this, archaeal RNA polymerase subunit numbers and assignments are quite similar to those of yeast (77,78). Three-dimensional similarities were borne out quite dramatically via X-ray crystallography of the archaeal enzymes from Sulfolobus solfataricus and Sulfolobus shibatae (two species of a thermoacidophile genus from the kingdom Crenarchaeota) in the presence and absence of DNA (3,4,79) and the enzyme from Thermococcus kodakarensis (from the kingdom Euryarchaeota [5]).…”

Subunit D of RNA Polymerase from Methanosarcina acetivorans Contains Two Oxygen-labile [4Fe-4S] Clusters

“…The catalytic subunit Rpb1 and the auxiliary subunits Rpb4 -10 and Rbp12 then assemble to form complete Pol II. Similarly, the assembly of archaeal RNAP is initiated by the formation of a heterodimer of subunits D and L followed by the addition of subunits N and P, forming the DLNP assembly platform (42). A stable BDLNP subcomplex that is competent in DNA binding and transcription factor interaction has also been identified, indicating that subunit B is likely added prior to the addition of the core AЈ and AЉ subunits and auxiliary HKFE subunits (10).…”

“…A stable BDLNP subcomplex that is competent in DNA binding and transcription factor interaction has also been identified, indicating that subunit B is likely added prior to the addition of the core AЈ and AЉ subunits and auxiliary HKFE subunits (10). Subunit B is split into two polypeptides (BЈ and BЉ) in some Euryarchaeota, including M. acetivorans (42).…”

The Sulfolobus Initiator Element Is an Important Contributor to Promoter Strength

“…A rchaeal transcription shares remarkable similarities with the eukaryotic process, and archaeal RNA polymerase (RNAP) has multiple components that are homologous with the subunits of the eukaryal type II RNAP (1). In contrast to eukaryotes, which use multiple general transcription factors (GTFs), each with a complex composition, archaea depend on 2 intrinsic GTFs in transcription initiation: the TATA box binding protein (TBP) and transcription factor B (TFB) (2,3).…”