Journal:Science:1

Structural basis of transcription activation

Yu Feng, Yu Zhang, Richard H. Ebright ^[1]

Molecular Tour
Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)–promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises Thermus thermophilus transcription activator protein TTHB099 (TAP) [homolog of Escherichia coli catabolite activator protein (CAP)], T. thermophilus RNAP σ^A holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.

TAP, RNAP holoenzyme, DNA and RNA.

DNA/RNA/protein interactions.

To obtain a structure of TAP-RPo, we used a nucleic-acid scaffold corresponding to positions –57 to +15 (-54 to +11 shown) of a class II TAP-dependent promoter (positions numbered relative to transcription start site). Pink, nontemplate strand; red, template strand. The scaffold contained a consensus DNA site for TAP centered between positions –41 and –42 (TAP site: cyan, template strand; deeppink, nontemplate strand), a near-consensus extended –10 element (violet), a consensus –10 element (blue), a consensus discriminator element (royalblue), a consensus core recognition element, a 13-bp transcription bubble (maintained in the unwound state by having noncomplementary sequences on nontemplate and template strands), and UpCpGpA (in magenta).

Comparison of TAP-DNA in TAP-RPo to CAP-DNA. TAP in cyan, CAP in skyblue. Click here to see animation of this scene.

Protein-DNA interactions

• TAP binding. TAP is in cyan/dodgerblue. Pink, nontemplate strand; red, template strand.
• TAP binding (90° rotation).
• TAP site. TAP is in cyan, σ is in yellow. Pink, nontemplate strand; red, template strand.
• Interactions between σR4 and –35 region.
• Interactions between σR3 and extended –10 element (in violet).
• Interactions between σR2 consensus –10 element (in blue).
• Protein-DNA interactions that mediate promoter recognition.
• σ conserved region σR1.2 interacts with nontemplate-strand ssDNA of the discriminator element (in royalblue).
• DNA/RNA/protein interactions after the discriminator element.