Under physiological conditions, the ErmE methyltransferase
specifically modifies a single adenosine within ribosomal
RNA (rRNA), and thereby confers resistance to multiple
antibiotics. The adenosine (A2058 in Escherichia coli
23S rRNA) lies within a highly conserved structure, and
is methylated efficiently, and with equally high fidelity,
in rRNAs from phylogenetically diverse bacteria. However,
the fidelity of ErmE is reduced when magnesium is removed,
and over twenty new sites of ErmE methylation appear in
E. coli 16S and 23S rRNAs. These sites show widely
different degrees of reactivity to ErmE. The canonical
A2058 site is largely unaffected by magnesium depletion
and remains the most reactive site in the rRNA. This suggests
that methylation at the new sites results from changes
in the RNA substrate rather than the methyltransferase.
Chemical probing confirms that the rRNA structure opens
upon magnesium depletion, exposing potential new interaction
sites to the enzyme. The new ErmE sites show homology with
the canonical A2058 site, and have the consensus sequence
aNNNcgGAHAg (ErmE methylation occurs exclusively
at adenosines (underlined); these are preceded by a guanosine,
equivalent to G2057; there is a high preference for the
adenosine equivalent to A2060; H is any nucleotide except
G; N is any nucleotide; and there are slight preferences
for the nucleotides shown in lower case). This consensus
is believed to represent the core of the motif that Erm
methyltransferases recognize at their canonical A2058 site.
The data also reveal constraints on the higher order structure
of the motif that affect methyltransferase recognition.