The mechanism of RNA binding to TRAP: Initiation and cooperative interactions
- 1 January 2001
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 7 (1) , 85-93
- https://doi.org/10.1017/s135583820100173x
Abstract
The trp RNA-binding Attenuation Protein (TRAP) from Bacillus subtilis is an 11-subunit protein that binds a series of 11 GAG and UAG repeats separated by two to three-spacer nucleosides in trp leader mRNA. The structure of TRAP bound to an RNA containing 11 GAG repeats shows that the RNA wraps around the outside of the protein ring with each GAG interacting with the protein in nearly identical fashion. The only direct hydrogen bond interactions between the protein and the RNA backbone are to the 2′-hydroxyl groups on the third G of each repeat. Replacing all 11 of these guanosines with deoxyriboguanosine eliminates measurable binding to TRAP. In contrast, a single riboguanosine in an otherwise entirely DNA oligonucleotide dramatically stabilizes TRAP binding, and facilitates the interaction of the remaining all-DNA portion with the protein. Studies of TRAP binding to RNAs with between 2 and 11 GAGs, UAGs, AAGs, or CAGs showed that the stability of a TRAP-RNA complex is not directly proportional to the number of repeats in the RNA. These studies also showed that the effect of the identity of the residue in the first position of the triplet, with regard to binding to TRAP, is dependent on the number of repeats in the RNA. Together these data support a model in which TRAP binds to RNA by first forming an initial complex with a small subset of the repeats followed by a cooperative interaction with the remaining triplets.Keywords
This publication has 27 references indexed in Scilit:
- A Bacillus subtilis Gene of Previously Unknown Function, yhaG , Is Translationally Regulated by Tryptophan-Activated TRAP and Appears To Be Involved in Tryptophan TransportJournal of Bacteriology, 2000
- Probing the TRAP–RNA interaction with nucleoside analogsRNA, 1999
- Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNANature, 1999
- TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcriptsJournal of Biological Chemistry, 1994
- Thermodynamic and alkylation interference analysis of the lac repressor-operator substituted with the analog 7-deazaguanineBiochemistry, 1993
- Interactions between the trp repressor and its operator sequence as studied by base analog substitutionBiochemistry, 1992
- Functional contacts of a transfer RNA synthetase with 2′-hydroxyl groups in the RNA minor grooveNature, 1992
- An apparent Bacillus subtilis folic acid biosynthetic operon containing pab, an amphibolic trpG gene, a third gene required for synthesis of para-aminobenzoic acid, and the dihydropteroate synthase geneJournal of Bacteriology, 1990
- cis-acting sites in the transcript of the Bacillus subtilis trp operon regulate expression of the operonJournal of Bacteriology, 1988
- Relationships between apparent binding energies measured in site-directed mutagenesis experiments and energetics of binding and catalysisBiochemistry, 1988