Escherichia coli 6S RNA represents a non-coding RNA (ncRNA), which, based on the 
conserved secondary structure and previous functional studies, had been 
suggested to interfere with transcription. Selective inhibition of sigma-70 
holoenzymes, preferentially at extended -10 promoters, but not 
stationary-phase-specific transcription was described, suggesting a direct role 
of 6S RNA in the transition from exponential to stationary phase. To elucidate 
the underlying mechanism, we have analysed 6S RNA interactions with different 
forms of RNA polymerase by gel retardation and crosslinking. Preferred binding 
of 6S RNA to Esigma(70) was confirmed, however weaker binding to Esigma(38) was 
also observed. The crosslinking analysis revealed direct contact between a 
central 6S RNA sequence element and the beta/beta' and sigma subunits. Promoter 
complex formation and in vitro transcription analysis with exponential- and 
stationary-phase-specific promoters and the corresponding holoenzymes 
demonstrated that 6S RNA interferes with transcription initiation but does not 
generally distinguish between exponential- and stationary-phase-specific 
promoters. Moreover, we show for the first time that 6S RNA acts as a template 
for the transcription of defined RNA molecules in the absence of DNA. In 
conclusion, this study reveals new aspects of 6S RNA function.