Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3

Abstract

The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves 16S rRNA between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3 that activate the 16S rRNA for 2′ OH induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and Helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.

Bacteriocins and their position in the next wave of conventional antibiotics

“…Members of the E-group endonuclease colicins have the H-N-H motif and bind the BtuB/Tol translocation machinery in order to cross the outer membrane [56,57]. These bacteriocins cleave the 16S rRNA at the 3'-end of the coding sequence, which inhibits translation [18,54,57]. It does so by accumulation of sequential impaired decoding events that results in low occupancy at the A site and inability to elongate the peptide past the first few codons.…”

“…Specifically, colicins E3, E4 and E6 and cloacin DF13 show 16S rRNase activity [54,55]. DNase and RNase mechanisms of action have been identified in the colicin family (E2, E7, E8 and E9; and D, E3, E4, E5, E6 and cloacin DF13, respectively) [19,[54][55][56][57][58].…”

“…DNase and RNase mechanisms of action have been identified in the colicin family (E2, E7, E8 and E9; and D, E3, E4, E5, E6 and cloacin DF13, respectively) [19,[54][55][56][57][58]. Members of the E-group endonuclease colicins have the H-N-H motif and bind the BtuB/Tol translocation machinery in order to cross the outer membrane [56,57].…”

Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF

“…The immunity protein is lost during colicin translocation to the cytoplasm (14), with cell death resulting through one of three nuclease activities (8). ColE3, ColE4, and ColE6 are rRNases that inhibit protein synthesis through site-specific cleavage of a single phosphodiester bond within the A-site of 30S ribosomal RNA (15,16). ColE5 is a tRNase that blocks protein synthesis through the cleavage of the anticodon loops of a subset of tRNAs (17).…”

Ribosomal Encoded Bacteriocins: Their Functional Insight and Applications

“…In these systems, bacteriocin appears to be bound and transported by a single outer membrane protein. Ribosomal encoded bacteriocins having nucleases activity fall into two groups, those which have nonspecific activity like DNase and those which have specific activity like RNase [30]. Most of these nuclease bacteriocins elicit cell death through either hydrolases or transferases by targeting phosphodiester bonds in the bacterial cytoplasm [31].…”