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Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics

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  • Authors: Soyeong Sim1, Sandra L. Wolin2
  • Editors: Gisela Storz3, Kai Papenfort4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702; 2: RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702; 3: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD; 4: Department of Biology I, Microbiology, LMU Munich, Martinsried, Germany
  • Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0023-2018
  • Received 26 January 2018 Accepted 05 March 2018 Published 06 July 2018
  • Sandra L. Wolin, [email protected]
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  • Abstract:

    Y RNAs are noncoding RNAs (ncRNAs) that are present in most animal cells and also in many bacteria. These RNAs were discovered because they are bound by the Ro60 protein, a major target of autoantibodies in patients with some systemic autoimmune rheumatic diseases. Studies of Ro60 and Y RNAs in , the first sequenced bacterium with a Ro60 ortholog, revealed that they function with 3′-to-5′ exoribonucleases to alter the composition of RNA populations during some forms of environmental stress. In the best-characterized example, Y RNA tethers the Ro60 protein to the exoribonuclease polynucleotide phosphorylase, allowing this exoribonuclease to degrade structured RNAs more effectively. Y RNAs can also function as gates to regulate access of other RNAs to the Ro60 central cavity. Recent studies in the enteric bacterium serovar Typhimurium resulted in the discovery that Y RNAs are widely present in bacteria. Remarkably, the most-conserved subclass of bacterial Y RNAs contains a domain that mimics tRNA. In this review, we discuss the structure, conservation, and known functions of bacterial Y RNAs as well as the certainty that more bacterial Y RNAs and additional roles for these ncRNAs remain to be uncovered.

  • Citation: Sim S, Wolin S. 2018. Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics. Microbiol Spectrum 6(4):RWR-0023-2018. doi:10.1128/microbiolspec.RWR-0023-2018.

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/content/journal/microbiolspec/10.1128/microbiolspec.RWR-0023-2018
2018-07-06
2018-09-21

Abstract:

Y RNAs are noncoding RNAs (ncRNAs) that are present in most animal cells and also in many bacteria. These RNAs were discovered because they are bound by the Ro60 protein, a major target of autoantibodies in patients with some systemic autoimmune rheumatic diseases. Studies of Ro60 and Y RNAs in , the first sequenced bacterium with a Ro60 ortholog, revealed that they function with 3′-to-5′ exoribonucleases to alter the composition of RNA populations during some forms of environmental stress. In the best-characterized example, Y RNA tethers the Ro60 protein to the exoribonuclease polynucleotide phosphorylase, allowing this exoribonuclease to degrade structured RNAs more effectively. Y RNAs can also function as gates to regulate access of other RNAs to the Ro60 central cavity. Recent studies in the enteric bacterium serovar Typhimurium resulted in the discovery that Y RNAs are widely present in bacteria. Remarkably, the most-conserved subclass of bacterial Y RNAs contains a domain that mimics tRNA. In this review, we discuss the structure, conservation, and known functions of bacterial Y RNAs as well as the certainty that more bacterial Y RNAs and additional roles for these ncRNAs remain to be uncovered.

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Figures

Image of FIGURE 1
FIGURE 1

Predicted secondary structures of a human Y RNA and the experimentally identified bacterial Y RNAs. (A) Human Y3 RNA. Modules involved in binding Ro60 and effector proteins are indicated. The portion of the stem containing the Ro60 binding site can form an alternative conformer containing a conserved bulged helix ( 16 ). In the structure of Y3 complexed with Ro60 ( 25 ), the bases shown in green (GGUCCGA) are sites of specific interactions with the Ro60 protein. (B, C) Yrn1 and Yrn2. The sequences that can form the conserved helix are boxed, and the conserved “metazoan motif” GGUCCGA is colored in green. An adenine nucleotide that may represent the second A in the “bacterial motif” is colored orange. On Yrn1, regions for Rsr binding and PNPase binding are indicated. (D, E) Typhimurium YrlA and YrlB. The GNCGAANG motif is in orange. (F, G) YrlA and YrlB. Nucleotides are colored as in panels D and E.

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0023-2018
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Image of FIGURE 2
FIGURE 2

Structures of Ro60 and Rsr proteins. (A) A molecular surface representation of Ro60 (PDB ID: 1YVR) colored by electrostatic surface potential. (B) A molecular surface representation of Rsr (PDB ID: 2NVO) colored by electrostatic surface potential. For both panels A and B, positive potentials are in blue and negative potentials are in red (–10 kT/e to 10 kT/e). (C) Structure of Ro60 bound to a misfolded 5S rRNA fragment (PDB ID: 2I91). The helix binds the basic outer surface and the single-stranded 3′ end binds in the hole. (D) Structure of Ro60 bound to a fragment of Y RNA stem containing the conserved sequences required for Ro60 binding (PDB ID: 1YVP). Positions of the 5′ and 3′ ends are indicated. Biochemical studies support a model in which other portions of the Y RNA contact a basic platform that overlaps with the misfolded RNA-binding site (dashed line) ( 25 , 29 ).

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0023-2018
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Image of FIGURE 3
FIGURE 3

YrlA RNAs contain a module that resembles tRNA. (A) Typhimurium YrlA presented to resemble a canonical tRNA. Highly conserved nucleotides between YrlA orthologs are colored orange, while conserved purines and pyrimidines are in blue. Bases shown to be modified ( 11 ) are indicated. AS, D, T, and V denote the acceptor stem, D arm, T arm, and variable arm, respectively. (B) tRNA-Ala-GCA. Nucleotides that are conserved between YrlA RNAs are in orange. All depicted tertiary interactions can potentially form in YrlA RNAs. (C) The genome-encoded sequence of YrlA drawn to emphasize the resemblance to tRNA. The structure of the acceptor stem after cleavage, end nibbling, and posttranscriptional CA addition ( 13 ) is also shown (arrow). Conserved nucleotides are colored as in panel A. (D) Yrn1 presented to resemble tRNA. Nucleotides in the T arm that are conserved between Yrn1 and YrlA RNAs are colored as in panel A.

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0023-2018
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Image of FIGURE 4
FIGURE 4

Phylogenetic trees of representative Rsr-containing bacterial species. (A) Phylogenetic tree based on the sequences of 16S rRNAs ( 70 ). Each phylum is represented by a distinct color. (B) Phylogenetic tree based on the sequences of Rsr proteins. Sequence alignments were performed using Clustal Omega ( 71 ), and trees were drawn with the Phylogeny Interference Package (PHYLIP) using the maximum likelihood method ( 72 ).

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0023-2018
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Image of FIGURE 5
FIGURE 5

Role of Yrn1 in scaffolding RYPER formation. (A) Yrn1, Rsr (PDB ID: 2NVO) (light blue), and PNPase (PDB ID: 1E3P) (pink). The Yrn1 modules that bind Rsr and PNPase are indicated. (B) The structure of RYPER predicted by single-particle electron microscopy and three-dimensional reconstruction ( 12 ) (EMDB ID: 5389). The density that likely corresponds to Yrn1 is colored in yellow, while densities corresponding to Rsr and PNPase are colored as in panel A. A possible path for degrading a structured RNA substrate, in which the 3′ end threads from Rsr into the PNPase cavity for degradation, is depicted in blue.

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