Domain V of Giardia lamblia large-subunit rRNA: structure of the peptidyl transferase loop from an early-branching eukaryote and correlation with antibiotic sensitivity

Abstract

Large subunit rRNA (LSR) sequences that have been implicated in peptide bond formation form a specific secondary structure called the peptidyl transferase loop (PTL). Although well conserved, the PTLs of eubacteria, archaebacteria, and eukaryotes have several distinct differences. These differences correlate with different sensitivities to peptidyl transferase and translocase inhibitors. To shed light on the basis for these kingdom-specific differences in PTL structure and function, we have analyzed the sequence and secondary structure of LSR domain V, which contains the PTL, from Giardia lamblia. This parasitic protozoan derives from a very early branch in eukaryotic evolution, and its rRNA was previously shown to have bacteria-like features. In vitro and cell-free systems were also used to test the sensitivity of G. lamblia protein synthesis to specific PTL-targeted inhibitors. Our results indicate that the PTL structure and inhibitor sensitivity typical of higher eukaryotes is conserved in G. lamblia. However, several adjacent domain V sequences more closely resemble archaebacterial rRNA, confirming the ‘primitive’ nature of G. lamblia rRNA. Thus, the eukaryotic PTL has been conserved over a vast evolutionary period. We speculate that the eukaryotic PTL is primordial and employs specific RNA-RNA interactions to catalyze protein synthesis. Three potential interactions were identified.