Identification of M-box RNAs located upstream of bacterial Nramp-related genes.

<p>(A) The magnesium riboswitch consists of two portions – a divalent-sensing aptamer and downstream sequences which couple the conformational status of the aptamer with formation of an intrinsic transcription termination site. An increase in intracellular magnesium triggers a compacted conformation of the aptamer domain <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004429#pgen.1004429-Ramesh1" target="_blank">[42]</a> and sequestration of an oligonucleotide tract that would otherwise disrupt terminator formation (“T”). Therefore, increased magnesium promotes transcription termination, repressing downstream gene expression. (B) We searched for instances of putative magnesium riboswitches located upstream of Nramp-related genes and identified many such occurrences. Two were identified for <i>Clostridium acetobutylicum</i> Nramp-related sequences, <i>Ca_c0685</i> and <i>Ca_c3329</i>, and are shown schematically herein. (C) To determine whether the <i>Ca_c0685</i> and <i>Ca_c3329</i> RNA elements were likely to function as magnesium riboswitches, the respective aptamer domains were incubated with varying magnesium and analyzed by analytical ultracentrifugation. Prior studies of the magnesium riboswitch revealed a striking compaction of the aptamer domain in response to magnesium <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004429#pgen.1004429-Dann1" target="_blank">[41]</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004429#pgen.1004429-Ramesh1" target="_blank">[42]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004429#pgen.1004429-Ramesh2" target="_blank">[49]</a>. The sedimentation velocity measurements of the <i>Ca_c0685</i> and <i>Ca_c3329</i> riboswitches revealed an identical compaction with magnesium, suggesting they are likely to function similar to the previously characterized riboswitch.