A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer

• Published in: eLife Vol. 8
• Main Authors: Atilho, Ruben M, Mirihana Arachchilage, Gayan, Greenlee, Etienne B, Knecht, Kirsten M, Breaker, Ronald R
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 05.04.2019; eLife Sciences Publications, Ltd
• Subjects: Antifungal agents; Aptamers; Aptamers, Nucleotide - metabolism; Bacillus subtilis - genetics; Bacillus subtilis - metabolism; Bacteria; Biochemistry and Chemical Biology; Bioinformatics; Diphosphates - metabolism; Enzymes; Gene expression; Gene Expression Regulation, Bacterial; gene regulation; Genomes; Ligands; Nucleic Acid Conformation - drug effects; pseudoknot; Pyrimidines - metabolism; Ribonucleic acid; Riboswitch; Riboswitches; RNA; RNA polymerase; RNA transcription; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; Sulfur; Sulfuric Acid Esters - metabolism; thiamin pyrophosphate; Thiamine; Thiamine - biosynthesis; Thiamine diphosphate; Transcription; Vitamin B; United States > US; thiamin pyrophosphate; chemical biology; pseudoknot; gene regulation; RNA transcription; biochemistry; E. coli
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.45210

We recently implemented a bioinformatics pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA structures in bacteria. A prominent candidate revealed by our initial search efforts was called the ' motif' because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P. In the current report, we describe biochemical and genetic data demonstrating that motif RNAs function as sensors of the thiamin precursor HMP-PP, which is fused with HET-P ultimately to form the final active coenzyme thiamin pyrophosphate (TPP). HMP-PP riboswitches exhibit a distinctive architecture wherein an unusually small ligand-sensing aptamer is almost entirely embedded within an otherwise classic intrinsic transcription terminator stem. This arrangement yields remarkably compact genetic switches that bacteria use to tune the levels of thiamin precursors during the biosynthesis of this universally distributed coenzyme.