Abstract
Most bacterial ribonucleases (RNases) known to date have been identified in either Escherichia coli or Bacillus subtilis. These two organisms lie on opposite poles of the phylogenetic spectrum, separated by 1-3 billion years of evolution. As a result, the RNA maturation and degradation machineries of these two organisms have little overlap, with each having a distinct set of RNases in addition to a core set of enzymes that is highly conserved across the bacterial spectrum. In this paper, we describe what the functions performed by major RNases in these two bacteria, and how the evolutionary space between them can be described by two opposing gradients of enzymes that fade out and fade in, respectively, as one walks across the phylogenetic tree from E. coli to B. subtilis.
Highlights
When the sequence of the Bacillus subtilis genome was completed in 1997, its completeness was questioned by scientific colleagues who found it difficult to accept that the gene encoding the essential and most important ribonuclease in Escherichia coli in terms of numbers of substrates (RNase E), was missing
The full genome sequence led to the realisation that was the gene encoding RNase E absent from B. subtilis, but of the ∼15 ribonucleases known in E. coli at that time, only a handful had homologs in B. subtilis (RNase P, RNase III, RNase PH, PNPase, and RNase R)
In addition to degrading RNA, RNases can paradoxically stabilize RNA, by eliminating nucleotides that could potentially recruit degradative enzymes. This is typically the case for the so-called stable RNAs, e.g. ribosomal RNA and transfer RNA, that are generally synthesized in the form of precursors that are trimmed at both their 5 and 3 ends to yield the final stable and functional molecules [8]
Summary
E. coli and B. subtilis use overlapping strategies but very different enzymes to degrade their mRNAs. In E. coli, the key RNase that makes the first endoribonucleolytic cut is RNase E, a low specificity enzyme with a preference for AU-rich single stranded (ss) regions, with a strong preference for a U-residue at +2 relative to the cleavage site [12] It is essential in E. coli and is associated with the inner membrane via an amphipathic helix downstream of the N-terminal catalytic half of the protein [13]. RNase II, which likely evolved from a duplication of the RNase R gene, is well conserved in the γand β-Proteobacteria, but only occurs sporadically outside of these two classes All of these 3 exoribonucleases typically cannot degrade RNAs all the way to mononucleotides and fall off the substrates when they are in the range of 2–10 nts [18]. RNase J is highly conserved from the α-Proteobacteria all the way through to the Mollicutes and Firmicutes, where its gene was duplicated to produce RNase J1 and J2
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