Variation in phylogenetic tendencies of contiguous riboswitches

Riboswitches are widely distributed RNA regulatory elements primarily found in prokaryotes. Over a decade ago, it was discovered that certain genes are regulated either by multiple tandemly arranged riboswitches or by riboswitches with tandem sensor domains.Riboswitches consist of a sensor domain, also known as an aptamer, and an expression platform, primarily regulating gene expression through transcription or translation attenuation, although other mechanisms such as RNA splicing or stability modulation are also possible. In tandemly arranged riboswitches, the first riboswitch is often positioned far from the ribosome binding site of the target gene, making transcriptional regulation a likely primary mechanism. In contrast, riboswitches with adjacent aptamers have a single expression platform, which may be located at varying distances from the regulated gene. Consequently, no inherent bias towards either transcriptional or translational regulation is expected in this case.Considering the reported enrichment of transcriptional riboswitches in certain phylogenetic clades, the present study analyses the distribution of tandemly arranged riboswitches and riboswitches with adjacent aptamers across various phylogenetic groups, as well as the tendencies of different riboswitch families to regulate genes in a contiguous fashion. Our results indicate that Bacillota is the phylum with the most notable families of tandemly arranged riboswitches. In contrast, regulation of gene expression via tandem sensor domains was predominantly associated with the Pseudomonadota phylum. On the other hand, our statistical analysis identified the T-box and cyclic dimeric guanosine monophosphate as the most prominent members of tandemly arranged riboswitches, while the glycine riboswitch is the most relevant family to be composed of adjacent aptamers.In addition, this article presents a comprehensive analysis of all relevant orthologous gene groups regulated by contiguous riboswitches, highlighting trends in cases where strict regulation is necessary due to the high metabolic cost of a pathway. Finally, we provide an in-depth discussion of the observed regulatory tendencies.