Antisense-acting Riboswitch Regulates Transcriptional Regulator

We identified an antisense-acting c-di-GMP-I riboswitch [51 (link)] regulating the paen-P40081_02330 gene coding a transcriptional regulator of the XRE family in the Paenibacillus sp. FSL P4 genome (Fig 2E). This transcriptional regulator, whose nearest homolog is SinR, a transcriptional repressor known as the master regulator for biofilm formation in Bacillus subtilis, controls the expression of genes involved in exopolysaccharide, matrix protein production, and motility.
The synthesis of signaling molecules is one strategy bacteria employ to sense alterations in their environment in order to rapidly adjust according to those changes. One of these molecules is the bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP), which is able to induce the transition from a unicellular motile state to a multicellular sessile state through phosphorelay systems that control biofilm and spore formation (Fig 2E) [52 (link)–55 (link)].
For many bacteria, the quorum-sensing intercellular communication mechanism is essential for gene expression pattern coordination at the population level. Furthermore, for motility, biofilm matrix production, and spore formation processes, quorum sensing is critical, as it is one of the main strategies to sense and respond to environmental changes (Fig 2E) [56 (link)–59 (link)].
The c-di-GMP-I antisense-acting riboswitch regulation of a transcription factor coded by the paen-P40081_02330 gene that we propose is based on the detection of this molecule, triggering the expression of the genes involved in biofilm and spore formation, as well as quorum-sensing processes, and having a general effect on their expression when it is not sensed, thanks to its close relationship with the master regulator of these processes, Spo0A (Fig 2E).
As mentioned above, in the literature, there are only two examples of the regulation of gene expression mediated by riboswitches that act in an opposite direction, one of which is the cobalamin antisense-acting riboswitch identified at the 3`end of the gene encoding the PocR transcriptional regulator of the enzymes involved in the metabolism of propanediol in L. monocytogenes, the enzymes of which require cobalamin as a cofactor to be active. In our study, we identified cobalamin antisense-acting riboswitches in the orthologous pocR genes of other Listerias and in the Enterococcaceae Vagococcus carniphilus. The regulation of genes encoding transcription factors (TFs) makes it possible to extend the regulatory outcome of the riboswitches that act in an opposite direction to multiple functionally related genes in different operons, which have in common the operator site of the corresponding TFs. In our study, the c-di-GMP-I, cobalamin, and TPP antisense-acting riboswitches were the most frequent riboswitches of this group.