Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?

Abstract

Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries.

Keywords: genetic regulation; non-coding RNA; small RNAs.

Figure 1

Number of distinct annotated sRNAs per bacterial strain in Proteobacteria. The iceberg is intended to be a graphical representation of the knowledge we have about the prevalence of sRNAs in Proteobacteria (gray section) as opposed to what we could be missing (hatched section). The ratio of the surface versus underwater portions of the iceberg is proportional to results represented in the graph, where the gray region is what is known (i.e., the visible part of the iceberg), and the hatched area under that region is what could be left to discover (that is, the underwater section of the iceberg). Percentages also represent this ratio. This figure represents a compilation of 2629 strains. Only sRNAs with an E-value lower than 0.0005 were considered.

Figure 2

Top 20 bacterial species with the highest number of distinct annotated sRNAs in (A) Proteobacteria and in (B) bacteria from the Terrabacteria group. Species denoted with “sp.” represent instances where only the genus of the bacteria was noted. It can be observed that in (A), all species are from the same family, Enterobacteriaceae. In (B), species from different orders are emphasized by their own color. The number of distinct sRNAs considers all strains for each species. Only sRNAs with an E-value lower than 0.0005 were considered.

Figure 3

Top 20 sRNAs annotated in bacteria. Each individual occurrence of sRNAs were counted, even if some were found multiple times within the same genome. Only sRNAs with an E-value lower than 0.0005 were taken into consideration.

Figure 4

Number of annotated genes and RNAs in bacteria. Data required for the creation of this graph were taken from RiboGap [15]. (A) The number of annotated genes is graphed according to the genome size, which comprises all chromosomes and plasmids of each individual strain if applicable. (B) The number of annotated RNAs is graphed according to the “fragment size”, which considers chromosomes and plasmids separately for each individual strain. RNAs are not limited only to sRNAs but also include CRISPR RNAs, antisense RNAs, sRNAs, long non-coding RNAs (lncRNAs), rRNAs, ribozymes, tRNAs and cis-regulatory elements. Species from Terrabacteria group and Proteobacteria that were found to have the most annotated sRNAs (Figure 2) are represented by black and blue dots, respectively; all other strains are shown in gray.