Genetic disruption of the bacterial <i>raiA</i> motif noncoding RNA causes defects in sporulation and aggregation.

Abstract

Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the "<i>raiA</i> motif" has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the <i>raiA</i> and <i>comFC</i> genes of many species of Bacillota and Actinomycetota. Structural probing of the <i>raiA</i> motif RNA from the Gram-positive anaerobe <i>Clostridium acetobutylicum</i> confirms key features of its sophisticated secondary structure model. Expression analysis of <i>raiA</i> motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The <i>raiA</i> motif RNA becomes the fourth most abundant RNA in <i>C. acetobutylicum</i>, excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the <i>raiA</i> motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a <i>raiA</i> motif gene from a plasmid. These results demonstrate that <i>raiA</i> motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.