We have identified proteins that control the expression of slpA, the gene encoding the crystalline surface layer of Thermus thermophilus HB8. We cloned three genes from T. thermophilus that specifically repressed the expression of the slpA promoter in Escherichia coli. The proteins encoded by two of them (Rep6 and Rep29) bound in vitro to the slpA promoter, while that from the third (Rep54) bound specifically to the 5'-untranslated region (5'UTR) of the slpA mRNA. Rep6 protein was identified as a C-fragment from a Thermus cytoplasmic basic protein of 28 kDa, whose coding gene, slrA (for S-layer regulator), was characterized. Surprisingly, Rep29 was identified as a C-fragment of SlpM, an S-layer-like protein that is overexpressed in slpA mutants. Insertional inactivation of slrA and slpM demonstrated their in vivo function in the control of slpA transcription: SlrA acts as a repressor, and SlpM as an activator. Even more surprising was the identification of Rep54, the 5'UTR mRNA-binding protein, as a C-terminal fragment of the SlpA protein. This result, in addition to further in vivo evidence presented here, supports the existence of a translational autoregulation in slpA expression. The physiological meaning of overlapping transcriptional and translational controls of S-layer expression, and its relationships with other systems, are discussed.