Chapter 28 : Origin, Evolution, and Loss of Bacterial Small RNAs

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As our understanding of the transcriptional landscape of bacteria continues to expand, it has become clear that noncoding small RNAs (sRNAs) play a pivotal regulatory role ( ). Typically 50 to 400 nucleotides in length, sRNAs posttranscriptionally regulate gene expression, usually by base-pairing with one or more mRNA targets ( ). sRNAs likely provide certain advantages over protein regulators because they act quickly, are relatively metabolically inexpensive, and provide an additional way to respond to environmental signals ( ). Beyond these basic characteristics, however, the roles of bacterial sRNAs are extremely diverse: they are capable of upregulating or downregulating translation, stabilizing mRNAs or targeting them for degradation, sharing targets, and/or targeting multiple mRNAs. Variability in their sequence, structure, and how and when they are transcribed allows them to meet a wide range of nuanced regulatory needs based on the diverse environments to which bacteria must adapt.

Citation: Dutcher H, Raghavan R. 2019. Origin, Evolution, and Loss of Bacterial Small RNAs, p 487-497. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0004-2017
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Figure 1

sRNA origin, functional divergence, and loss. (a) sRNA sources include duplication events, HGT, and origination via promoter emergence. (b) Sequence and structural changes are often accompanied by differential sRNA gene expression and accumulation of mRNA targets and/or protein-binding regions, causing the sRNA to become fully integrated into regulatory networks. (c) sRNA loss occurs through mutations that erode promoter sequences, genome rearrangements that split sRNA-containing IGRs, and selective pressures that prompt shifts in network interactions.

Citation: Dutcher H, Raghavan R. 2019. Origin, Evolution, and Loss of Bacterial Small RNAs, p 487-497. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0004-2017
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Figure 2

Sequence conservation and structure of an sRNA gene. (a) Sequence conservation within an sRNA gene (orange) and flanking protein-coding genes (blue). The black line represents nucleotide diversity index, π, calculated using a sliding-window analysis; the flanking green lines indicate the 95% confidence interval. Lowest nucleotide polymorphism within sRNA genes is observed in mRNA-binding regions. (b) Predicted structure of an sRNA, showing a single-stranded mRNA-binding site and a terminator hairpin. Adapted from reference with permission.

Citation: Dutcher H, Raghavan R. 2019. Origin, Evolution, and Loss of Bacterial Small RNAs, p 487-497. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0004-2017
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