The 5′ untranslated region (UTR) of the long-lived
Escherichia coli ompA transcript functions as
an mRNA stabilizer that can prolong the cytoplasmic lifetimes
of a variety of messages to which it is fused. Previous
studies have identified two domains of this 5′ UTR
that together are responsible for its stabilizing effect.
One is a 5′-terminal stem-loop. The other is a single-stranded
RNA segment (ss2) that contains a ribosome binding site
highly complementary to 16S ribosomal RNA. Here we report
a detailed investigation of the function of these two stabilizing
elements. Our data indicate that mRNA protection by a 5′
stem-loop requires no sequence features or thermodynamic
stability beyond the minimum necessary for stem-loop formation.
Stabilization by ss2 appears to result not from a high
frequency of translation initiation, but rather from a
high degree of occupancy of this 5′ UTR segment by
bound ribosomes. Although close spacing of translating
ribosomes is not critical for message stabilization by
the ompA 5′ UTR, mRNA longevity does require
the periodic passage of ribosomes through the protein-coding
region. Unlike bound ribosomes, which hinder mRNA cleavage
by RNase E, the 5′ stem-loop appears to impede degradation
of ompA mRNA via a distinct pathway that is RNase
E-independent. These findings imply that the ompA
5′ UTR prolongs mRNA longevity by impeding multiple
pathways for mRNA degradation.