Genome‐wide Discovery of Rare Riboswitches in Bacteria

Abstract

Riboswitches are noncoding RNAs (ncRNAs) that directly sense specific ligands and regulate various metabolic and physiological pathways. More than 40 different classes of riboswitches have been experimentally validated, and hundreds of additional novel riboswitch classes are predicted to remain to be discovered and analyzed. We are exploiting an improved computational pipeline that can be used to comprehensively uncover novel structured ncRNAs in bacteria, including rare riboswitches. Comprehensive analysis of long and GC‐rich intergenic regions in five different bacterial genomes yielded nearly 70 novel genetic element candidates, including 30 putative ncRNA motifs. Among these novel ncRNA classes, five are considered strong riboswitch candidates. One of the riboswitch candidates, called the thiS motif, has now been experimentally proven to regulate thiamin biosynthesis by directly sensing 2‐methyl‐4‐amino‐5‐hydroxymethylpyrimidine pyrophosphate (HMP‐PP). The mechanistic studies of this HMP‐PP riboswitch demonstrate that the nascent RNA transcript undergoes a conformational change from an ‘on’ state to an ‘off’ state during the transcription process. HMP‐PP binding stabilizes the riboswitch aptamer in its ‘on’ conformation. Experimental validation of the HMP‐PP riboswitch also indicates that the existing bioinformatics pipeline can now be exploited to discover the vast majority of structured ncRNAs hidden among hundreds of sequenced bacterial genomes.Support or Funding InformationHigh‐performance computing at the Yale Center for Research Computing is supported in part by Yale University and by NIH S10RR029676. R.M.A was supported by the National Science Foundation Graduate Research Fellowship Program (DGE1122492). This work was supported by the National Institutes of Health grants (GM022778, DE022340) to R.R.B. Research in the Breaker laboratory is also supported by the Howard Hughes Medical Institute.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.