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Functional and structural characterization of the glycine riboswitch
Author(s) -
Ye Jingdong,
Elsayed Galal,
Elsayed Mohammed,
Brinda Bryan,
Zhang Wei,
Stoner Breena
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.653.6
Subject(s) - aptamer , cooperativity , riboswitch , glycine , chemistry , linker , cooperative binding , binding site , biophysics , biochemistry , stereochemistry , biology , microbiology and biotechnology , gene , amino acid , gene expression , computer science , non coding rna , operating system
Glycine riboswitch is unique in that the two glycine aptamers bind glycines cooperatively and control downstream gene expression in a more “digital” manner. The exact structural mechanism for this glycine binding cooperativity is not well understood. We hypothesize that the cooperativity is caused by the formation of “Aptamer Disruptor” in the absence of glycine, which involves an interaction between “b” region (on aptamer I) and “c” region (on aptamer II). In‐line probing data on a 5’ extended aptamer II shows reduced glycine binding activity compared to a previously reported aptamer II construct VCII122, consistent with this hypothesis. Sequence analysis identified the candidate regions of “b” and “c”. Breaker Lab reported that VC G17C completely abolished the aptamer I and reduced the aptamer II glycine binding by 1000 fold. According to our hypothesis, this is at least in part due to b/c interaction. Data on a double mutant, VCG17CM1, in which the b/c interaction was abolished by mutation in “b” region, shows that binding of VCG17CM1 with glycine is rescued compared to VCG17C, suggesting the direct involvement of “b” region in the formation of “Aptamer Disruptor”. Further experiment is being carried out to test the “c” region, the linker region and other important locations. We are also crystallizing the glycine riboswitch using a chaperone approach (CARC; Ye et al. PNAS 2008) for detailed structural elucidation. Source of research support: start‐up fund provided to JD Ye from University of Central Florida.