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In Streptococcus thermophilus, the locus rggC contains a frameshift mutation and thus consists of two open reading frames (ORFs), rggC1 and rggC2, which encode proteins exhibiting similarity with the Rgg transcriptional regulator family. In this work, mutants showing a partial deletion of rggC1 and rggC2 were constructed and their response to menadione, a superoxide-generating compound, was analysed. These mutants exhibited different behaviour to this oxidative stress compared with the wild-type strain. Analysis of this locus among 21 strains of S. thermophilus showed a polythymine tract length variability and a strain-dependant adenine residue could be found upstream of this repeat. This interstrain polymorphism supports evidence for the hypothesis that the rggC locus is phase variable.