Fig 1.
Models of the putative regulatory mechanisms of RNA polymerases transcribing in opposite directions.
(A) RNA polymerase collision; (B) asRNA/mRNA duplex formation: (1) partially synthesized double-stranded RNA, (2) totally synthesized double-stranded RNA; (C) DNA supercoil accumulation. Representative elements are colored as follows: mRNA transcription complex, blue; asRNA transcription complex, pink; SD sequence, yellow. Created with BioRender.com.
Table 1.
Tendency of riboswitch families to act in an antisense orientation.
Table 2.
Frequency of genes potentially regulated by antisense-acting riboswitches.
Fig 2.
Representative pathways of genes regulated by antisense-acting riboswitches.
(A) Gene encoding an enzyme involved in the interconversion of a compound related to the metabolite sensed by the riboswitch; (B) Gene encoding an enzyme that requires a cofactor sensed by the riboswitch to become active or participates in a metabolic pathway wherein another enzyme requires the cofactor; (C) Gene encoding a transporter protein for a compound related to the metabolite sensed by the riboswitch; (E) Gene that codes for a transcriptional regulator. Metabolic route active in the presence (yellow) or absence (green) of the metabolite sensed (red circle) by the antisense-acting riboswitch. Representative elements are colored as follows: Target genes, blue; antisense-acting riboswitch, violet. Enzymes are indicated by rectangles; compounds are indicated by ovals. Created with BioRender.com.
Fig 3.
Representative syntenic context of genes regulated by antisense-acting riboswitches.
The upper panel on each section shows in detail an example of the different types of genes regulated by the antisense-acting riboswitches, while the lower panel shows the context in closely related organisms compared to the example. (A) Gene coding for a transposase: COG2138-Uncharacterized conserved protein, COG1648-Siroheme synthase, COG0733-Na+-dependent transporters of the SNF family, COG0739-Membrane proteins related to metalloendopeptidases; (B) Pseudogene: COG0041-Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase, COG0026-Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase), COG0015-Adenylosuccinate lyase; (C) Gene coding for an uncharacterized ORF with clear orthologs in multiple genomes; (D) Hypothetical small gene without orthologs: COG2261-Predicted membrane protein, COG0210-Superfamily I DNA and RNA helicases, CO1115-Na+/alanine symporter, COG0053-Predicted Co/Zn/Cd cation transporters. Representative elements are colored as follows: Riboswitch spuriously regulated genes, blue; antisense-acting riboswitch, violet; bona fide regulated gene, pink. Genes are colored according to the COG they belong to. Created with BioRender.com.