Np₄A alarmones function in bacteria as precursors to RNA caps.

Abstract

Stresses that increase the cellular concentration of dinucleoside tetraphosphates (Np₄Ns) have recently been shown to impact RNA degradation by inducing nucleoside tetraphosphate (Np₄) capping of bacterial transcripts. However, neither the mechanism by which such caps are acquired nor the function of Np₄Ns in bacteria is known. Here we report that promoter sequence changes upstream of the site of transcription initiation similarly affect both the efficiency with which <i>Escherichia coli</i> RNA polymerase incorporates dinucleoside polyphosphates at the 5' end of nascent transcripts in vitro and the percentage of transcripts that are Np₄-capped in <i>E. coli</i>, clear evidence for Np₄ cap acquisition by Np₄N incorporation during transcription initiation in bacterial cells. <i>E. coli</i> RNA polymerase initiates transcription more efficiently with Np₄As than with ATP, particularly when the coding strand nucleotide that immediately precedes the initiation site is a purine. Together, these findings indicate that Np₄Ns function in bacteria as precursors to Np₄ caps and that RNA polymerase has evolved a predilection for synthesizing capped RNA whenever such precursors are abundant.