I sat down with the RA yesterday, planning to look for riboswitches in her E. coli sxy mRNA sequence. But a couple of discoveries made this unnecessary.
First, she reminded me that Vibrio cholerae has two sxy homologs, not just one, and we quickly realized that the c-di-GMP ('GEMM') riboswitch is in the one that isn't known to have anything to do with competence.
We also checked the supplementary files for the paper that characterized this riboswitch, and discovered that the authors had done a very extensive search for GEMM riboswitches, not just in all the published bacterial genomes but in all microbial genomes and in a wide assortment of environmental genomics datasets. They found no GEMM riboswitches in any Pasteurellaceae; this isn't surprising because there's no evidence of c-di-GMP in this family. But they also found no GEMM riboswitches in any of the Enterobacteraceae.
So we decided that E. coli is very unlikely to regulate its sxy gene by a GEMM riboswitch.
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