NpA alarmones function in bacteria as precursors to RNA caps.

Stresses that increase the cellular concentration of dinucleoside tetraphosphates (NpNs) have recently been shown to impact RNA degradation by inducing nucleoside tetraphosphate (Np) capping of bacterial transcripts. However, neither the mechanism by which such caps are acquired nor the function of NpNs 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 RNA polymerase incorporates dinucleoside polyphosphates at the 5' end of nascent transcripts in vitro and the percentage of transcripts that are Np-capped in , clear evidence for Np cap acquisition by NpN incorporation during transcription initiation in bacterial cells. RNA polymerase initiates transcription more efficiently with NpAs than with ATP, particularly when the coding strand nucleotide that immediately precedes the initiation site is a purine. Together, these findings indicate that NpNs function in bacteria as precursors to Np caps and that RNA polymerase has evolved a predilection for synthesizing capped RNA whenever such precursors are abundant.