Operons of ribosomal proteins of E.coli are a well known example of autoregulation of transcription initiation based on RNA secondary structures. These structures are conserved in other enterobacteria. In this study we analyzed operons of ribosomal proteins in the completely sequenced of a more distantly related gamma-proteobacterium H.influenzae.

We have identified operons of ribosomal proteins in H.influenzae using published annotations and GOLDIE 2.0 software for identification of orthologous gene strings and then analyzed secondary structures of RNA. We have found conserved RNA structures in three operons.

Operon alpha is controlled by binding of S4 to a pseudoknot structure at start of gene rpsM encoding protein S13. The structure involving high order interactions is identical in E.coli and H.influenzae, whereas the other regions share structural, but not sequence similarity.

Operon S15 consists of a single gene rpsO encoding S15. This operon is autoregulated by formation of alternative structures: either a pair of hairpins or a pseudoknot. It is interesting to note that only part of the extensive secondary structure found in E.coli is conserved in H.influenzae, but it is exactly the domain experimentally proven to be recognized by S15.

Operon spc is controlled by binding of S8 at the start of gene rplE encoding L5. The binding site is a hairpin resembling the S8 binding site in 16S rRNA. In fact, two different structures can be formed both in E.coli and H.influenzae, both of which are corroborated by complementary substitutions. Thus it is plausible that some sort of alternative structure formation is involved in translation regulation of this operon.

This study was partially supported by a grant from the Russian Foundation for Basic Research.