The 2.1-Å crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box

Abstract

Archaea possess a basal transcriptional apparatus that resembles that of eukaryotes. Here we report the 2.1-Å crystal structure of the archaeal transcription factor complex formed by the TATA-box-binding protein (TBP), the transcription factor IIB homolog, and a DNA target, all from the hyperthermophile Pyrococcus woesei. The overall fold of these two basal transcription factors is essentially the same as that of their eukaryotic counterparts. However, in comparison with the eukaryotic complexes, the archaeal TBP-DNA interface is more symmetrical, and in this structure the orientation of the preinitiation complex assembly on the promoter is inverted with respect to that seen in all crystal structures of comparable eukaryotic systems. This study of the structural details of an archaeal transcription factor complex presents the opportunity to examine the evolution of the basal eukaryotic transcriptional apparatus from a stereochemical viewpoint and to extend our understanding of the physical biochemistry of transcriptional initiation.The recent sequencing of the first archaeal genome has confirmed the designation of the archaea as a third kingdom of life, distinct from eubacteria and eukaryotes (1). Recent discoveries indicate that the basal components of transcription in archaea resemble those in the eukaryotic RNA polymerase II transcriptional system (2). Archaeal homologs to the transcription factors TATA-box binding protein (TBP) and transcription factor IIB (TFIIB) have been reported (3-6). As in eukaryotic polymerase II transcription, archaeal transcription is initiated by an AϩT-rich TATA-like segment known as the "boxA" sequence, containing a consensus T C TTA T A ANN (hereafter referred to as the boxA͞TATA element) (7,8). Interestingly, one of the common archaeal promoter sequences contains the boxA͞TATA element, TTTATATA, which is an inverted canonical eukaryotic TATA box (8). Like eukaryotic TBP, archaeal TBP recognizes the boxA͞TATA element, and transcription factor B (TFB) from Pyrococcus woesei (pwTFB) binds to the TBP-DNA complex (3). Homologs to other eukaryotic basal transcription factors, or TBP-associated factors (TAFs), however, are not present in the archaeal genome. In fact, promoter-specific transcription can occur in a purified reconstituted archaeal system, with only TBP, TFB, and polymerase (9).We present here the 2.1-Å crystal structure of the ternary archaeal transcription complex, illustrating the interaction of TBP, TFB, and a promoter fragment. The components are all from P. woesei, a hyperthermophilic archaeon which exhibits an optimal growth temperature of 105°C (10). The amino acid sequence of pwTBP is 36-41% identical to the conserved C-terminal core of its eukaryotic counterparts (3), and, as expected from this degree of homology, we have recently found that the general features of its three-dimensional structure are the same as those of eukaryotic TBP (11). pwTFB is 28-32% identical to full-length eukaryotic TFIIBs, and 25% identical to the C-terminal domain of the yeas...

Transcription Factor B Contacts Promoter DNA Near the Transcription Start Site of the Archaeal Transcription Initiation Complex

“…2 and 3). The results are as expected based on the crystallographic structures of TBP-DNA and TBP-TFBc-DNA complexes (27,28) and on DNase I footprinting experiments with archaeal TBP-DNA and TBP-TFBc-DNA complexes (7,11,13). The results are similar to published results for eukaryal initiation complexes (43,44,59), supporting the homology between the two transcription systems.…”

“…Archaeal TFB belongs to the TFIIB family, whose members bind promoter DNA, bind RNAP, and serve as bridges between the TBP-TATA-element complex and RNAP (26 -29). Archaeal TFB has the characteristic domain organization of other TFIIB family members (31, 32), comprising a C-terminal domain (TFBc) that mediates interactions with the TBP-TATA-element complex (7,27,28) and an N-terminal domain (TFBn) that mediates interactions with RNAP (33,34). The TFB N-terminal domain consists of a conserved metal binding region ("zinc ribbon"; Refs.…”

Mercury Inactivates Transcription and the Generalized Transcription Factor TFB in the Archaeon Sulfolobus solfataricus

“…The archaeal general transcription apparatus is homologous to the eukaryotic Pol II system but is simpler (25,27,41). Archaea contain a single RNA polymerase composed of 12 subunits orthologous to those in eukaryotes (25). Archaeal promoters have architecture similar to that of eukaryotic Pol II promoters, consisting of a TATA box located 26 nucleotides upstream from the transcription start site (36).…”

“…Archaeal metabolic genes show similarity with those of bacterial prokaryotes; however, biochemical and genomic studies indicate that they use mechanisms like those of eukaryotes for many subcellular processes, including transcription (7). The archaeal general transcription apparatus is homologous to the eukaryotic Pol II system but is simpler (25,27,41). Archaea contain a single RNA polymerase composed of 12 subunits orthologous to those in eukaryotes (25).…”

Erratum: Emergence of symbiosis in peptide self-replication through a hypercyclic network

“…In both, the RNA polymerase contains the large universal subunits and five smaller subunits found in both Archaea and eukaryotes. Transcription initiation is a simplified version of the eukaryotic mechanism 28,29 . However, A. fulgidus alone has a homologue of eukaryotic TBP-interacting protein 49 not seen in M. jannaschii, but apparently present in Sulfolobus solfactaricus.…”