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The structural basis for terminator recognition by the Rho transcription termination factor.
C E Bogden1, D Fass, N Bergman
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Massachusetts 02142, USA.
Molecular Cell
|May 7, 1999
Summary
The Rho protein terminates bacterial transcription by binding RNA. Its RNA-binding domain structure reveals sequence specificity, explaining its preference for cytosine-rich RNA and suggesting a model for Rho hexamer function.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- The Rho protein is essential for transcription termination in bacteria like E. coli.
- It disengages newly transcribed RNA from the DNA template.
- Understanding Rho's RNA-binding mechanism is key to deciphering transcription regulation.
Purpose of the Study:
- To determine the X-ray crystal structure of the RNA-binding domain of E. coli Rho.
- To elucidate the structural basis for Rho's RNA sequence specificity.
- To propose a model for the allosteric regulation of the Rho hexamer.
Main Methods:
- X-ray crystallography was used to determine the structure of the Rho RNA-binding domain complexed with an RNA ligand.
- Analysis of the crystal structure revealed specific features of the RNA-binding site.
- Computational modeling was employed to develop a model for the intact Rho hexamer.
Main Results:
- The crystal structure identified filters within the RNA-binding site that confer sequence specificity.
- These filters explain Rho's preference for cytosine-rich RNA.
- Crystal packing showed two Rho domain protomers binding a single RNA with a single base spacer, suggesting a mechanism for strong RNA binding.
Conclusions:
- The structure of the Rho RNA-binding domain provides insights into its sequence recognition capabilities.
- The findings suggest that RNA-binding module pairing contributes to Rho's affinity for RNA.
- A model of subunit dimerization on an asymmetric ligand explains allosteric control in the Rho hexamer.