Structure-based search reveals hammerhead ribozymes in the human microbiome.
Deep sequencing of viral or bacterial nucleic acids monitors the presence and diversity of microbes in select populations and locations. Metagenomic study of mammalian viromes can help trace paths of viral transmissions within or between species. High throughput sequencing of patient and untreated sewage microbiomes showed many sequences with no similarity to genomic sequences of known function or origin. To estimate the distribution of functional RNAs in these microbiomes, we used the hammerhead ribozyme (HHR) motif to search for sequences capable of assuming its three-way junction fold. Although only two of the three possible natural HHR topologies had been known, our analysis revealed highly active ribozymes that terminated in any of the three stems. The most abundant of these are type II HHRs, one of which is the fastest natural cis-acting HHR yet discovered. Altogether, 13 ribozymes were confirmed in vitro, but only one showed sequence similarity to previously described HHRs. Sequences surrounding the ribozymes do not generally show similarity to known genes, except in one case, where a ribozyme is immediately preceded by a bacterial RadC gene. We demonstrate that a structure-based search for a known functional RNA is a powerful tool for analysis of metagenomic datasets, complementing sequence alignments.
From the Departments of Pharmaceutical Sciences.
Randi M
RM
Jimenez
the Blood Systems Research Institute and; Department of Laboratory Medicine, University of California, San Francisco, California 94118.
Eric
E
Delwart
From the Departments of Pharmaceutical Sciences,; Chemistry, and; Molecular Biology and Biochemistry, University of California, Irvine, California 92697 and. Electronic address: aluptak@uci.edu.
Andrej
A
Lupták
D001483:Base Sequence; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D008969:Molecular Sequence Data; D016337:RNA, Catalytic / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
D016337:RNA, Catalytic; C427204:hammerhead ribozyme
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