The TATA-Binding Protein: a General Transcription Factor in Eukaryotes and Archaebacteria

Rowlands, Tracey; Baumann, Peter; Jackson, Stephen

doi:10.1126/science.8191287

Cited by 173 publications

(144 citation statements)

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“…Taken together, these data strongly support the function of RBP2 to be that of a transcription factor. In addition, the interaction between RBP2 and TBP (Kim et al, 1994), an essential component of general transcriptional machinery (Rowlands et al, 1994), is further evidence that RBP2 functions as a transcription factor.…”

Section: Discussionmentioning

confidence: 99%

T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2

1997

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The LIM domain protein rhombotin-2 (RBTN-2/TTG-2/ Lmo2) has distinct functions in erythropoiesis and in Tcell leukemogenesis. Additional functions for RBTN2 are indicated by its expression in non-hematopoietic tissues. These diverse functions of RBTN2 are presumed to be accomplished through physical interaction with dierent protein partners that bind the LIM domains of RBTN2. To identify these proteins which may modulate the activity of RBTN2, a human cDNA library was screened using the yeast two-hybrid assay. Using the RBTN2 LIM domain region as`bait', the retinoblastoma-binding protein 2 (RBP2) was identi®ed as a partner for RBTN2. The interaction between RBTN2 and RBP2 was con®rmed using in vitro binding assays, and by coimmunoprecipitation of the two proteins. Deletion analysis showed the second LIM domain of RBTN2 was necessary and sucient for binding to the last 69 amino acids of RBP2. The interaction between RBTN2 and RBP2 had a functional consequence: the combination of RBP2 and RBTN2 gave higher transcription in vitro, than RBTN2 alone. The interaction with RBP2 suggests two additional functions for RBTN2: (i) RBTN2 may directly aect the activity of RBP2, and/ or (ii) RBTN2 may indirectly modulate the functions of the retinoblastoma protein by binding to RBP2.

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Section: Discussionmentioning

confidence: 99%

T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2

1997

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“…Archaeal and eukaryal general transcription factors also exhibit striking structural homology (24 -29). Archaeal TBP belongs to the family of TATA-element-binding proteins that bind to promoter TATA elements, bend DNA, and nucleate the formation of initiation complexes (24,25,30). 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).…”

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confidence: 99%

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

Renfrow

Naryshkin

Lewis

et al. 2004

Journal of Biological Chemistry

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Transcription initiation in all three domains of life requires the assembly of large multiprotein complexes at DNA promoters before RNA polymerase (RNAP)-catalyzed transcript synthesis. Core RNAP subunits show homology among the three domains of life, and recent structural information supports this homology. General transcription factors are required for productive transcription initiation complex formation. The archaeal general transcription factors TATA-element-binding protein (TBP), which mediates promoter recognition, and transcription factor B (TFB), which mediates recruitment of RNAP, show extensive homology to eukaryal TBP and TFIIB. Crystallographic information is becoming available for fragments of transcription initiation complexes (e.g. RNAP, TBP-TFB-DNA, TBP-TFIIB-DNA), but understanding the molecular topography of complete initiation complexes still requires biochemical and biophysical characterization of protein-protein and protein-DNA interactions. In published work, systematic site-specific protein-DNA photocrosslinking has been used to define positions of RNAP subunits and general transcription factors in bacterial and eukaryal initiation complexes. In this work, we have used systematic site-specific protein-DNA photocrosslinking to define positions of RNAP subunits and general transcription factors in an archaeal initiation complex. Employing a set of 41 derivatized DNA fragments, each having a phenyl azide photoactivable crosslinking agent incorporated at a single, defined site within positions ؊40 to ؉1 of the gdh promoter of the hyperthermophilic marine archaea, Pyrococcus furiosus (Pf), we have determined the locations of PfRNAP subunits PfTBP and PfTFB relative to promoter DNA. The resulting topographical information supports the striking homology with the eukaryal initiation complex and permits one major new conclusion, which is that PfTFB interacts with promoter DNA not only in the TATA-element region but also in the transcription-bubble region, near the transcription start site. Comparison with crystallographic information implicates the PfTFB N-terminal domain in the interaction with the transcription-bubble region. The results are discussed in relation to the known effects of substitutions in the TFB and TFIIB N-terminal domains on transcription initiation and transcription start-site selection.Extensive structural and biochemical characterization of transcription initiation complexes has revealed similarity of transcription systems across the three domains of life (1-4). Transcription initiation in archaea closely resembles eukaryal class II transcription initiation and is mediated by a single RNA polymerase (RNAP) 1 and two general transcription factors, TATA-element binding protein (TBP) and transcription factor B (TFB) (5, 6). In vitro transcription initiation has been demonstrated with RNAP, TBP, and TFB in Pyrococcus (7-10), Methanococcus (11), Methanosarcina (12), and Sulfolobus (13) cell-free transcription systems.Recent crystallographic structures of bacterial RNAP and eukary...

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“…Evidence from sequence similarity studies between RNA polymerases suggests that archaeal transcription shared certain components with that of the Eukarya (Puhler et al 1989), a conclusion further supported by the discovery of TFIIB in Pyrococcus furiosus (Ouzounis and Sander 1992) and TBP in P. woesei (Rowlands et al 1994). The strong similarity of archaeal transcription initiation factors with their eukaryotic counterparts has reinforced the concept that these domains shared an ancestral transcriptional apparatus.…”

Section: Introductionmentioning

confidence: 59%

“…Moreover, the minimal set of factors required for in vitro transcription initiation in archaea consists of TATA-box binding protein (TBP), TFIIB and RNA polymerase II (Werner and Weinzierl 2002). In bacteria, however, the process appears to be fundamentally different (Struhl 1999), with regulation accomplished by an entirely different set of proteins (Gralla 1996).Evidence from sequence similarity studies between RNA polymerases suggests that archaeal transcription shared certain components with that of the Eukarya (Puhler et al 1989), a conclusion further supported by the discovery of TFIIB in Pyrococcus furiosus (Ouzounis and Sander 1992) and TBP in P. woesei (Rowlands et al 1994). The strong similarity of archaeal transcription initiation factors with their eukaryotic counterparts has reinforced the concept that these domains shared an ancestral transcriptional apparatus.…”

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confidence: 75%

Lineage‐specific partitions in archaeal transcription

Coulson

Touboul

Ouzounis

2006

Archaea

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SummaryThe phylogenetic distribution of the components comprising the transcriptional machinery in the crenarchaeal and euryarchaeal lineages of the Archaea was analyzed in a systematic manner by genome-wide profiling of transcription complements in fifteen complete archaeal genome sequences. Initially, a reference set of transcription-associated proteins (TAPs) consisting of sequences functioning in all aspects of the transcriptional process, and originating from the three domains of life, was used to query the genomes. TAP-families were detected by sequence clustering of the TAPs and their archaeal homologues, and through extensive database searching, these families were assigned a function. The phylogenetic origins of archaeal genes matching hidden Markov model profiles of protein domains associated with transcription, and those encoding the TAP-homologues, showed there is extensive lineage-specificity of proteins that function as regulators of transcription: most of these sequences are present solely in the Euryarchaeota, with nearly all of them homologous to bacterial DNA-binding proteins. Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone-modifying enzymes also display extensive taxon-restrictedness, both across and within the two phyla. Keywords: genome profiling, protein families, sequence clustering, transcription-associated proteins. IntroductionTranscription, a core gene expression process, involves different agents participating in initiation, elongation, termination and regulation. The basic principles of transcriptional regulation in the Bacteria and Eukaryota have been outlined (Ptashne and Gann 1997), contrasting with the Archaea, where such mechanisms are less well-understood. The study of the archaeal transcriptional machinery is important to an understanding of both the molecular mechanisms, and the evolutionary history, of transcriptional regulation in all three domains of life. Furthermore, these analyses may reveal how archaea respond to environmental challenges, in particular, given their possible association with various aspects of human disease (Eckburg et al. 2003). Several previous studies have shown that the RNA polymerase core enzyme exhibits structural similarity between the Archaea and the Eukaryota (Puhler et al. 1989). Moreover, the minimal set of factors required for in vitro transcription initiation in archaea consists of TATA-box binding protein (TBP), TFIIB and RNA polymerase II (Werner and Weinzierl 2002). In bacteria, however, the process appears to be fundamentally different (Struhl 1999), with regulation accomplished by an entirely different set of proteins (Gralla 1996).Evidence from sequence similarity studies between RNA polymerases suggests that archaeal transcription shared certain components with that of the Eukarya (Puhler et al. 1989), a conclusion further supported by the discovery of TFIIB in Pyrococcus furiosus (Ouzounis and Sander 1992) and TBP in P. woesei (Rowlands et al. 1994). The strong similarity of archaeal...

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The TATA-Binding Protein: a General Transcription Factor in Eukaryotes and Archaebacteria

Cited by 173 publications

References 45 publications

T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2

T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2

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

Lineage‐specific partitions in archaeal transcription

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