Chapter 30 : Large Noncoding RNAs in Bacteria

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Although bacteria harbor far fewer long noncoding RNAs (ncRNAs) than eukaryotes, the known classes of large, structured ncRNAs in bacteria perform essential roles in the core processes of information transfer, metabolism, and physiological adaptation ( ). For example, many classes are central to genetic information processing: rRNAs act as ribozymes ( ) to translate mRNAs, RNase P ribozymes process precursor tRNAs ( ), transfer-messenger RNAs (tmRNAs) rescue stalled ribosomes ( ), and riboswitches bind ions and metabolites to regulate gene expression ( ). Furthermore, most of the large, structured ncRNA classes whose functions are known operate as ribozymes that perform essential chemical reactions such as peptide bond formation ( ), RNA splicing ( ), and RNA cleavage ( ). Two of these ribozyme classes, namely group I and group II introns, are sometimes components of selfish genetic elements that both splice mRNAs and mobilize to various regions in DNA genomes ( ). Of course, many self-splicing ribozymes also carry protein-coding regions, located either in their exon flanks or inserted into noncritical portions of their ribozyme structure. However, these coding regions are usually incidental to the main functions performed by the ncRNA’s structure. Collectively, these ncRNAs have an enormous influence on both genetic and cellular processes, which suggests the intriguing possibility that newly found large ncRNA classes may also serve fundamental roles in biology.

Citation: Harris K, Breaker R. 2019. Large Noncoding RNAs in Bacteria, p 515-526. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0005-2017
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Figure 1

Size and structural complexity of large and highly structured ncRNAs in bacteria. Structural complexity is represented by the number of multistem junctions and pseudoknots present in the predicted secondary-structure models, as described previously ( ). Overlapping points representing different ncRNAs are depicted with split circles. Narrowly distributed ncRNAs and ncRNAs with <2 multistem junctions and pseudoknots were omitted. For example, noncoding RNAs such as large sRNAs and clustered regularly interspaced short palindromic repeat (CRISPR) RNAs are commonly >200 nucleotides long but have repetitive and simple hairpin secondary structures that are bound by proteins. Although 23S rRNA forms the active site for the peptidyltransferase reaction catalyzed by ribosomes, 16S rRNA functions in complex with the catalytic RNA component and is classified accordingly.

Citation: Harris K, Breaker R. 2019. Large Noncoding RNAs in Bacteria, p 515-526. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0005-2017
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Figure 2

Consensus sequence and secondary-structure model for OLE RNAs. This model is based on the alignment of 657 unique representatives from genomic sequences from RefSeq version 63 and metagenomic sequences as described in reference . R and Y represent purine and pyrimidine nucleotides, respectively.

Citation: Harris K, Breaker R. 2019. Large Noncoding RNAs in Bacteria, p 515-526. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0005-2017
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Figure 3

Consensus sequence and secondary-structure model for GOLLD RNAs. This model is based on the alignment of sequences identified in reference . Notable predicted substructures include 2 E-loops, 3 GNRA tetraloops, and 5 pseudoknots. Of the 20 hairpin loops, 5 form pseudoknots or represent GNRA tetraloops. A total of 12 of the remaining 15 hairpin loops carry highly conserved nucleotides, suggesting that they might be involved in forming RNA tertiary contacts that are important for the function of GOLLD RNA. Other annotations are as described for Fig. 2 .

Citation: Harris K, Breaker R. 2019. Large Noncoding RNAs in Bacteria, p 515-526. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0005-2017
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Table 1

Large ncRNAs in bacteria with unpublished functions

Citation: Harris K, Breaker R. 2019. Large Noncoding RNAs in Bacteria, p 515-526. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0005-2017

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