Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Abstract

The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs.

Large Noncoding RNAs in Bacteria

“…Three additional putative classes of large ncRNAs, called OLE (17), GOLLD (18), and HEARO (18), have been investigated to some degree, but their biochemical roles are not well understood. Another 18 possible large ncRNA classes were recently discovered by using bioinformatics and await experimental validation (19). If all of these candidates indeed represent additional classes of large ncRNAs, establishing their functions would increase the number of large ncRNA activities in bacteria by four fold.…”

“…For example, comparative sequence analysis algorithms have been used to identify multiple novel classes of riboswitches (19–23) and ribozymes (24, 25), as well as exceptionally large and structurally complex ncRNAs (17, 18, A. Roth, Z. Weinberg, K. Vanderschuren, M. H. Murdock, E. Poiata, and R. R. Breaker, unpublished data). Each of the ncRNA classes discussed below was uncovered computationally through such phylogenetic analyses.…”

“…Recently, at least 16 candidate large ncRNA classes have been reported as part of a collection of 224 structured RNA motifs (19), which add to the list of candidates reported previously (18). The most noteworthy classes are discussed below, whereas the remaining motifs are listed in Table 1.…”

“…The most noteworthy classes are discussed below, whereas the remaining motifs are listed in Table 1. Full descriptions of all these ncRNAs can be found in the previous publications describing their initial identification (17–19). …”

“…The ROOL (Rumen-Originating, Ornate, Large) RNAs were originally identified (19) among metagenomic DNA sequences isolated from cow rumen. A total of 397 distinct examples have been identified predominantly in the Lactobacillales and Clostridiales orders.…”