The N-terminal domain of TFIIB from Pyrococcus furiosus forms a zinc ribbon

Zhu, Wenlian; Zeng, Qiandong; Colangelo, Christopher M.; Lewis, Lundy; Summers, Michael F.; Scott, Robert A.

doi:10.1038/nsb0296-122

Cited by 136 publications

(104 citation statements)

References 39 publications

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“…Several crystal structures of TFIIB in complex with other PIC components have been solved (Bagby et al, 1995;Nikolov et al, 1995;Zhu et al, 1996;Bushnell et al, 2004). In addition recent findings have determined how TFIIB plays a central role in the PIC in transcription initiation and mediates interactions with TBP, DNA, RNAP II components, and TFIIF (Hampsey, 1998;Chen and Hampsey, 2004;Chen and Hahn, 2004;Hahn, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…The NLS of Sua7p Is Contained in the "Core" Region Structural analyses of TFIIB have defined distinct domains of the protein; an amino terminal domain that forms a zinc ribbon and interacts with RNAP II and TFIIF (Zhu et al, 1996;Chen and Hahn, 2003), a conserved B finger domain that also interacts with RNAP II (Bushnell et al, 2004) followed by a linker, and the core or central/carboxy terminal domain (Figure 3). The core domain consists of two alpha helical repeats that interact with TBP and promoter DNA (Bagby et al, 1995;Nikolov et al, 1995;Lagrange et al, 1998).…”

Section: Kap114p Imports Sua7p In Vivomentioning

confidence: 99%

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Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

Hodges

Leslie

Mosammaparast

et al. 2005

MBoC

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Nuclear import and export is mediated by an evolutionarily conserved family of soluble transport factors, the karyopherins (referred to as importins and exportins). The yeast karyopherin Kap114p has previously been shown to import histones H2A and H2B, Nap1p, and a component of the preinitiation complex (PIC), TBP. Using a proteomic approach, we have identified several potentially new cargoes for Kap114p. These cargoes include another PIC component, the general transcription factor IIB or Sua7p, which interacted directly with Kap114p. Consistent with its role as a Sua7p import factor, deletion of KAP114 led to specific mislocalization of Sua7p to the cytoplasm. An interaction between Sua7p and TBP was also detected in cytosol, raising the possibility that both Sua7p and TBP can be coimported by Kap114p. We have also shown that Kap114p possesses multiple overlapping binding sites for its partners, Sua7p, Nap1p, and H2A and H2B, as well as RanGTP and nucleoporins. In addition, we have assembled an in vitro complex containing Sua7p, Nap1p, and histones H2A and H2B, suggesting that this Kap may import several proteins simultaneously. The import of more than one cargo at a time would increase the efficiency of each import cycle and may allow the regulation of coimported cargoes. INTRODUCTIONIn eukaryotic cells the nucleocytoplasmic transport of most proteins and some RNAs is mediated by an evolutionarily conserved family of soluble transport factors, the karyopherins (also referred to as importins and exportins; reviewed in Weis, 2003;Harel and Forbes, 2004;Mosammaparast and Pemberton, 2004). After synthesis in the cytoplasm, most nuclear protein cargoes are bound by a member of the karyopherin family, through direct interaction with a nuclear localization sequence contained in the cargo protein. Transport through the nuclear pore complex occurs via transient interactions of the karyopherin with the NPC. Once in the nucleus, the karyopherin encounters a high concentration of RanGTP, which acts as a regulator of transport. Interaction of the karyopherin with RanGTP leads to dissociation of the karyopherin from its nuclear cargo (Weis, 2003;Harel and Forbes, 2004;Mosammaparast and Pemberton, 2004). In some circumstances, nuclear-binding partners of the cargo appear to also play a role in stimulating the dissociation of Kap and cargo (Senger et al., 1998;Lee and Aitchison, 1999;Pemberton et al., 1999). In yeast, there are 14 members of the karyopherin family, with Ͼ20 members in mammalian cells (Mosammaparast and Pemberton, 2004). Karyopherins appear to function in either nuclear import or nuclear export, with only two examples of a Kap that works in both directions (Weis, 2003;Harel and Forbes, 2004;Mosammaparast and Pemberton, 2004). In yeast, 11 members of the karyopherin family must import at least 1500 nuclear proteins, suggesting that each receptor must have many cargoes. To date specific transport receptor-cargo pairs have only been shown for ϳ30 cargoes; in addition the NLS sequences recognized by most Kaps is n...

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Section: Discussionmentioning

confidence: 99%

Section: Kap114p Imports Sua7p In Vivomentioning

confidence: 99%

Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

Hodges

Leslie

Mosammaparast

et al. 2005

MBoC

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“…Its C-terminal domain interacts with TBP and DNA and constitutes a sequence-specific contact with the TFB-responsive element (BRE) immediately upstream of the TATA box (35) that is responsible for directing transcription in the same orientation as the eukaryotic complex (3). The N-terminal domain of TFB-1, containing a zinc ribbon (48), recruits RNA polymerase (4). Thus, inactivation of TFB-1 by HgCl 2 must disrupt either the formation of a ternary complex or the recruitment of RNAP or both.…”

Section: Discussionmentioning

confidence: 99%

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

Dixit

Bini

Drozda

et al. 2004

Antimicrob Agents Chemother

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Mercury has a long history as an antimicrobial agent effective against eukaryotic and prokaryotic organisms. Despite its prolonged use, the basis for mercury toxicity in prokaryotes is not well understood. Archaea, like bacteria, are prokaryotes but they use a simplified version of the eukaryotic transcription apparatus. This study examined the mechanism of mercury toxicity to the archaeal prokaryote Sulfolobus solfataricus. In vivo challenge with mercuric chloride instantaneously blocked cell division, eliciting a cytostatic response at submicromolar concentrations and a cytocidal response at micromolar concentrations. The cytostatic response was accompanied by a 70% reduction in bulk RNA synthesis and elevated rates of degradation of several transcripts, including tfb-1, tfb-2, and lacS. Whole-cell extracts prepared from mercuric chloride-treated cells or from cell extracts treated in vitro failed to support in vitro transcription of 16S rRNAp and lacSp promoters. Extract-mixing experiments with treated and untreated extracts excluded the occurrence of negative-acting factors in the mercury-treated cell extracts. Addition of transcription factor B (TFB), a general transcription factor homolog of eukaryotic TFIIB, to mercury-treated cell extracts restored >50% of in vitro transcription activity. Consistent with this finding, mercuric ion treatment of TFB in vitro inactivated its ability to restore the in vitro transcription activity of TFB-immunodepleted cell extracts. These findings indicate that the toxicity of mercuric ion in S. solfataricus is in part the consequence of transcription inhibition due to TFB-1 inactivation.The heavy metal mercury has been widely used as an antimicrobial agent for treatment of bacterial and fungal infections. At low levels, it is ubiquitous in the environment due to degassing of the earth's surface, while contamination by human activities, including its use in medicine and industry, have resulted in more concentrated occurrences (13). Mercury is a redox-active metal that depletes cellular antioxidants, particularly thiol-containing antioxidants, and enzymes in higher animals (15). Once absorbed into cells, both inorganic and organic types of mercury covalently bond with cysteine residues in proteins and small molecules. Although resistance to mercury has been intensively studied in bacteria, the mechanism of toxicity remains unclear. For example, RNA and protein syntheses in vivo have been reported to be inhibited by HgCl 2 (8), but in vitro analysis failed to detect an effect on general bacterial transcription (42). Additional support for the notion that mercury toxicity must be an important evolutionary force derives from the widespread phylogenetic and geographic distribution of mercury resistance genes. In contrast to the situation in bacteria, mercury is known to inhibit transcription in eukaryotes, reflecting action against a limited portion of the transcription apparatus. Immunofluorescence microscopy indicated that HgCl 2 blocked the synthesis of rRNA by RNA polymerase ...

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“…The TFB and TFIIB N-terminal domains each consists of a zinc ribbon (35,36,52) followed by a CSB. Available evidence suggests that the zinc ribbon is responsible for effects of TFB and TFIIB on recruitment of RNAP to initiation complexes (31,34,38,39) and that the CSB is responsible for effects of TFB and TFIIB on transcription-initiation NTP concentration dependence, transcription-initiation efficiency, and start-site selection (33,(37)(38)(39)(40)(41)(42).…”

Section: Ment Both In Thementioning

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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The N-terminal domain of TFIIB from Pyrococcus furiosus forms a zinc ribbon

Abstract: The three-dimensional structure of the N-terminal domain of an archaeal TFIIB, which has high sequence homology with eucaryal analogues, is strikingly similar to that of the C-terminal zinc ribbon of the eucaryal transcription elongation factor TFIIB.

Cited by 136 publications

References 39 publications

Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

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

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

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