DNA harvested directly from complex natural microbial communities
by PCR has been successfully used to predict RNase P RNA structure,
and can potentially provide an abundant source of information
for structural predictions of other RNAs. In this study, we
utilized genetic variation in natural communities to test and
refine the secondary and tertiary structural model for the
bacterial tmRNA. The variability of proposed tmRNA secondary
structures in different organisms and the lack of any predicted
tertiary structure suggested that further refinement of the
tmRNA could be useful. To increase the phylogenetic representation
of tmRNA sequences, and thereby provide additional data for
statistical comparative analysis, we amplified, sequenced, and
compared tmRNA sequences from natural microbial communities.
Using primers designed from gamma proteobacterial sequences,
we determined 44 new tmRNA sequences from a variety of
environmental DNA samples. Covariation analyses of these sequences,
along with sequences from cultured organisms, confirmed most
of the proposed tmRNA model but also provided evidence for a
new tertiary interaction. This approach of gathering sequence
information from natural microbial communities seems generally
applicable in RNA structural analysis.