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Molecular and genetic interactions of the RNA degradation machineries in Firmicute bacteria

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Correct balance between bacterial RNA degradation and synthesis is essential for controlling expression level of all RNAs. The RNA polymerase, which performs the RNA synthesis, is highly conserved across the bacterial domain. However, this is surprisingly not the case for the RNA degradation machinery, which is composed of different subunits and performs different enzymatic reactions, depending on the organism. In Escherichia coli, the RNA decay is performed by the degradosome complex, which forms around the membrane‐associated endoribonuclease RNase E, and is stable enough to be purified without falling apart. In contrast, many Firmicutes, for example, Bacillus subtilis, Staphylococcus aureus, and Streptococcus pneumoniae, do not encode an RNase E homolog, but instead have the endoribonuclease RNase Y and the exo‐ and endo‐ribonuclease RNase J complex. A wide range of experiments have been performed, mainly with B. subtilis and S. aureus, to determine which interactions exist between the various RNA decay enzymes in the Firmicutes, with the goal of understanding how RNA degradation (and thus gene expression homeostasis and regulation) is organized in these organisms. The in vivo and in vitro data is diverse, and does not always concur. This overview gathers the data on interactions between Firmicute RNA degradation factors, to highlight the similarities and differences between experimental data from different experiments and from different organisms. WIREs RNA 2018, 9:e1460. doi: 10.1002/wrna.1460 This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability
Alignment of BsCshA and SaCshA with domains indicated. Horizontal lines indicate predicted domains as used by Lehnik‐Habrink et al. () (for BsCshA) and Giraud et al. () (for SaCshA). Lines above and below the alignment refer to BsCshA and SaCshA, respectively. Both BsCshA and SaCshA have a long and poorly conserved C‐terminal extension and virtually no N‐terminal extension. Purple “DEAD” indicates the DEAD‐box motif
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The domain organization of RNase Y. The approximate regions are indicated with horizontal lines, based on BsY from Lehnik‐Habrink et al. (). Asterisks denote regions that participate in the dimer (or oligomer) formation. Purple Histidine‐Aspartate (HD) shows the active site residues. The alignment was shaded with BoxShade (http://www.ch.embnet.org/software/BOX_form.html)
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Crystal structure of Bacillus subtilis RNase J1 tetramer. Subunit (a) is shown as green sticks, and subunits (b) and (c) are shown in ribbon‐graphics with N‐termini in blue and C‐termini in red. The final subunit of the tetramer has been removed, to reveal the active site residues shown in yellow space‐filling graphics. The C‐termini of the (a) and (b) subunits intertwine in the A+B dimer, as do those of (c) and (d) (although subunit (d) is not shown). The figure was generated with the PDB file (3zq4) from Newman et al. ()
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RNase J1 and J2 are very similar. (a) An alignment of RNase J1 and J2 from Bacillus subtilis (BsJ1 and BsJ2, respectively) shows that they have many identical motifs, spread all along the length of the proteins. The residues that are part of the RNase J1 active site (Newman et al., ) are marked with purple. (b) Same as panel (a), but with RNase J1 and J2 from Staphylococcus aureus. The locations of the active site residues are based on the crystal structure of the B. subtilis RNase J1 (Newman et al., ), except for residues H74 and H76 in the HGH motif, for which functional analyses are also available for S. aureus (Hausmann et al., ; Linder, Lemeille, & Redder, ). Alignments were performed with Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/) and shaded with BoxShade (http://www.ch.embnet.org/software/BOX_form.html)
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RNase Y cleave transcripts encoding RNA decay factors in Staphylococcus aureus. Figure adapted from Khemici et al. () and Commichau et al. (). Bent black arrows indicate transcription initiation sites. Thick grey lines represent transcripts. Colored arrows show the coding sequences, with the corresponding encoded protein in the same color. Green arrowheads indicate SaY cleavage sites. (a) Transcript encoding SaJ2 (rnjB gene). (b) Transcript encoding SaPfk and pyruvate kinase (pfkA and pykA genes in purple and light grey, respectively). (c) Transcript encoding SaY (cvfA gene). (d) Transcript encoding SaRpoY and SaJ1 (rpoY and rnjA genes in pink and purple, respectively), three closely spaced but separate SaY cleavage sites are indicated (green “3”). (e) The gapR‐gap‐pgk‐tpi‐pgm‐eno transcript of S. aureus, encoding glycolytic operon regulator, glyceraldehyde‐3‐phosphate dehydrogenase, phosphoglycerate kinase, triosephosphate isomerase, phosphoglycerate mutase, and enolase (the gene order is the same in Bacillus subtilis, but the gene names are slightly different). The SaY cleavage site referred to in the text is indicated by a green arrowhead, and the approximate position of the BsY cleavage site on the equivalent B. subtilis transcript is shown with a red arrowhead. The two grey arrowheads indicate additional SaY cleavage sites, which have not been examined in B. subtilis. The subpanels are not to scale relative to each other
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Schematic overview of the main interactions within the network of the RNA degradation machinery. Each protein (or complex) is represented as a blob, and molecular interactions which have been observed in both Staphylococcus aureus and Bacillus subtilis are indicated by blobs that touch each other. Scissors indicate endoribonucleolytic activity and a “Pacman”‐shape indicates 5′ exonucleolytic activity. Unbroken arrows indicate genetic interactions, and dotted arrows indicate potential regulatory interactions. Certain potential interactions (e.g., those that involve PNPase and Pfk) have been left out for clarity
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Ribosomal proteins S2, S3, and S5 form a patch on the surface of the 30S ribosomal subunit. Proteins S2, S3, and S5 are shown in green, and cluster at the “top” of the 30S subunit, far from the 50S subunit. Other ribosomal proteins are in grey. The 16S rRNA is shown in cyan, and the 23S and 5S rRNAs are in blue and purple, respectively. The structure of the Staphylococcus aureus ribosome (PDB 5li0) was taken from Khusainov et al. () where the L1 protein was not modeled
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