Origins of Protein Stability Revealed by Comparing Crystal Structures of TATA Binding Proteins

Koike, Hideaki; Kawashima-Ohya, Yoshie; Yamasaki, Tomoko; Clowney, Lester; Katsuya, Yoshio; Suzuki, Masashi

doi:10.1016/j.str.2003.12.003

Cited by 15 publications

(29 citation statements)

References 41 publications

(2 reference statements)

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“…This residue allows the integration of cations in the protein–DNA interface (56) and a mutation of the residue leads to a decrease in affinity at higher salt concentrations. Both high temperature and high salt concentrations stabilize hydrophobic interactions (58,59) and this might explain the hydrophobic nature of the interior of thermophilic TBPs (60). Archaeal organisms counteract high external salt concentration with an increase in internal potassium levels.…”

Section: Discussionmentioning

confidence: 99%

Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways

Gietl

Holzmeister

Blombach

et al. 2014

Nucleic Acids Research

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During transcription initiation, the promoter DNA is recognized and bent by the basal transcription factor TATA-binding protein (TBP). Subsequent association of transcription factor B (TFB) with the TBP–DNA complex is followed by the recruitment of the ribonucleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are highly conserved in structure and function among the eukaryotic-archaeal domain but intriguingly have to operate under vastly different conditions. Employing single-pair fluorescence resonance energy transfer, we monitored DNA bending by eukaryotic and archaeal TBPs in the absence and presence of TFB in real-time. We observed that the lifetime of the TBP–DNA interaction differs significantly between the archaeal and eukaryotic system. We show that the eukaryotic DNA-TBP interaction is characterized by a linear, stepwise bending mechanism with an intermediate state distinguished by a distinct bending angle. TF(II)B specifically stabilizes the fully bent TBP–promoter DNA complex and we identify this step as a regulatory checkpoint. In contrast, the archaeal TBP–DNA interaction is extremely dynamic and TBP from the archaeal organism Sulfolobus acidocaldarius strictly requires TFB for DNA bending. Thus, we demonstrate that transcription initiation follows diverse pathways on the way to the formation of the pre-initiation complex.

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Section: Discussionmentioning

confidence: 99%

Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways

Gietl

Holzmeister

Blombach

et al. 2014

Nucleic Acids Research

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“…The interaction is hydrophobic: the amino acids affecting assembling of DM1 in either way are, in general, hydrophobic, whereas those having no effect are in general hydrophilic. In fact, I, V and L, positioned nearest to the assembling end, are the three key residues stabilizing hydrophobic interactions in the core of TATA‐binding protein (TBP) (Koike et al ., 2004b). The side‐chain volume of leucine is essentially the same as that of isoleucine, but its carbon atoms are stretched further outwards.…”

Section: Ligand‐mediated Transition Between Assemblies Of Dm1mentioning

confidence: 99%

Feast/famine regulatory proteins (FFRPs):Escherichia coliLrp, AsnC and related archaeal transcription factors

Yokoyama¹,

Ishijima²,

Clowney³

et al. 2006

FEMS Microbiol Rev

Self Cite

110

112

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Feast/famine regulatory proteins comprise a diverse family of transcription factors, which have been referred to in various individual identifications, including Escherichia coli leucine-responsive regulatory protein and asparagine synthase C gene product. A full length feast/famine regulatory protein consists of the N-terminal DNA-binding domain and the C-domain, which is involved in dimerization and further assembly, thereby producing, for example, a disc or a chromatin-like cylinder. Various ligands of the size of amino acids bind at the interface between feast/famine regulatory protein dimers, thereby altering their assembly forms. Also, the combination of feast/famine regulatory protein subunits forming the same assembly is altered. In this way, a small number of feast/famine regulatory proteins are able to regulate a large number of genes in response to various environmental changes. Because feast/famine regulatory proteins are shared by archaea and eubacteria, the genome-wide regulation by feast/famine regulatory proteins is traceable back to their common ancestor, being the prototype of highly differentiated transcription regulatory mechanisms found in organisms nowadays.

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“…TBP has a larger number of acidic residues than basic residues in M. jannaschii (34 acidic and 22 basic residues)21, an almost equal number of both charged residues in Sulfolobus acidocaldarius (22 acidic and 26 basic residues)22 and Pyrococcus woesei (26 acidic and 25 basic residues)23, and a smaller number of acidic residues than basic residues in Saccharomyces cerevisiae (15 acidic and 27 basic residues)24, Arabidopsis thaliana (15 acidic and 29 basic residues)25, and Homo sapiens (13 acidic and 29 basic residues)26 (Fig. 3B).…”

Section: Resultsmentioning

confidence: 99%

Uncovering ancient transcription systems with a novel evolutionary indicator

Adachi

Senda

Horikoshi

2016

Sci Rep

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TBP and TFIIB are evolutionarily conserved transcription initiation factors in archaea and eukaryotes. Information about their ancestral genes would be expected to provide insight into the origin of the RNA polymerase II-type transcription apparatus. In obtaining such information, the nucleotide sequences of current genes of both archaea and eukaryotes should be included in the analysis. However, the present methods of evolutionary analysis require that a subset of the genes should be excluded as an outer group. To overcome this limitation, we propose an innovative concept for evolutionary analysis that does not require an outer group. This approach utilizes the similarity in intramolecular direct repeats present in TBP and TFIIB as an evolutionary measure revealing the degree of similarity between the present offspring genes and their ancestors. Information on the properties of the ancestors and the order of emergence of TBP and TFIIB was also revealed. These findings imply that, for evolutionarily early transcription systems billions of years ago, interaction of RNA polymerase II with transcription initiation factors and the regulation of its enzymatic activity was required prior to the accurate positioning of the enzyme. Our approach provides a new way to discuss mechanistic and system evolution in a quantitative manner.

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Origins of Protein Stability Revealed by Comparing Crystal Structures of TATA Binding Proteins

Cited by 15 publications

References 41 publications

Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways

Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways

Feast/famine regulatory proteins (FFRPs):Escherichia coliLrp, AsnC and related archaeal transcription factors

Uncovering ancient transcription systems with a novel evolutionary indicator

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