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Identification of Spermidine Binding Site in T‐box Riboswitch Antiterminator RNA
Author(s) -
Liu Jia,
Zeng Chunxi,
Hogan Vivian,
Zhou Shu,
Monwar Md Masud,
Hines Jennifer V.
Publication year - 2016
Publication title -
chemical biology and drug design
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.59
H-Index - 77
eISSN - 1747-0285
pISSN - 1747-0277
DOI - 10.1111/cbdd.12660
Subject(s) - riboswitch , spermidine , identification (biology) , rna , rna binding protein , binding site , computational biology , chemistry , biology , biochemistry , non coding rna , gene , enzyme , botany
The T‐box transcription antitermination riboswitch controls bacterial gene expression by structurally responding to uncharged, cognate tRNA . Previous studies indicated that cofactors, such as the polyamine spermidine, might serve a specific functional role in enhancing riboswitch efficacy. As riboswitch function depends on key RNA structural changes involving the antiterminator element, the interaction of spermidine with the T‐box riboswitch antiterminator element was investigated. Spermidine binds antiterminator model RNA with high affinity (micromolar K d ) based on isothermal titration calorimetry and fluorescence‐monitored binding assays. NMR titration studies, molecular modeling, and inline and enzymatic probing studies indicate that spermidine binds at the 3′ portion of the highly conserved seven‐nucleotide bulge in the antiterminator. Together, these results support the conclusion that spermidine binds the T‐box antiterminator RNA preferentially in a location important for antiterminator function. The implications of these findings are significant both for better understanding of the T‐box riboswitch mechanism and for antiterminator‐targeted drug discovery efforts.