Sigma S(sigma(S)) encoded by rpoS in Escherichia coli is a stationary phase specific sigma subunit of the RNA polymerase holoenzyme. Widespread among the E coli K12 strains is an amber mutation that prematurely terminates as. These rpoSAm mutants would be expected to show no sigma(S) activity. However, suppressor free rpoSAm mutants retain an intermediate catalase activity, a sigma S controlled function. By analyzing the sequence of the rpoS gene we hypothesize that a 277 amino acids long A1-53sigma(S) of about 30kDa can be translated from an internal secondary translation initiation region (STIR, AGGGAGN(11)GUG) that is located downstream of the amber codon. By cloning this rpoSAm gene, following the expression, function, and N-terminal sequence of this mutant protein, we report the presence of a functional internal STIR in E coli rpoS, from where a truncated but nevertheless functional form of sigma(S) can be synthesized. (C) 2003 Elsevier Inc. All rights reserved.