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Regulation and functions of bacterial PNPase

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Polynucleotide phosphorylase (PNPase) is an exoribonuclease that catalyzes the processive phosphorolytic degradation of RNA from the 3′‐end. The enzyme catalyzes also the reverse reaction of polymerization of nucleoside diphosphates that has been implicated in the generation of heteropolymeric tails at the RNA 3′‐end. The enzyme is widely conserved and plays a major role in RNA decay in both Gram‐negative and Gram‐positive bacteria. Moreover, it participates in maturation and quality control of stable RNA. PNPase autoregulates its own expression at post‐transcriptional level through a complex mechanism that involves the endoribonuclease RNase III and translation control. The activity of PNPase is modulated in an intricate and still unclear manner by interactions with small molecules and recruitment in different multiprotein complexes. Not surprisingly, given the wide spectrum of PNPase substrates, PNPase‐defective mutations in different bacterial species have pleiotropic effects and perturb the execution of genetic programs involving drastic changes in global gene expression such as biofilm formation, growth at suboptimal temperatures, and virulence. WIREs RNA 2016, 7:241–258. doi: 10.1002/wrna.1328 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA Turnover and Surveillance > Regulation of RNA Stability
Structural similarities between PNPase, RNase PH, and the exosomes. (a) The homotrimeric structure of the EcPNPase (PDB ID: 3CDI) and the hexameric rings of RNase PH, archaeal, and eukaryotic exosomes (PDB ID: 1UDN, 2C37 and 2NN6, respectively) are reported. In the exosomes, only the subunits constituting the rings are shown in color and named (Box ). (b) Domain structure of bacterial PNPase.
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Legend on Next ColumnRegulation of PNPase expression. Detailed explanation of the model and supporting references are provided in the text. The pnp primary and processed transcripts have been drawn according to the most stable secondary structure predicted by mfold. Different regions of pnp mRNA are represented by lines of different colors: turquoise, pnp coding region; black, 5′‐UTR of the processed pnp mRNA; blue, stem‐loop removed by the RNase III staggered cuts; green, sRNA37. The 5′‐tri‐ and monophosphate ends of primary and processed RNAs, respectively, are indicated by the number of balls, and the 3′‐OH ends by arrowheads. Other symbols are explained in the box at the bottom of the figure. (a) The pnp primary transcript is translatable and stable in the absence of RNase III. PNPase acts as a translation repressor (┴), probably by competing with S1 ribosomal protein for mRNA binding. However, the native transcript is quickly processed by RNase III, which makes two staggered cuts in the long hairpin within the 5′‐UTR; (b) RNase III cleavage removes about half of the stem loop; the processed pnp mRNA with the small RNA37 annealed at its 5′‐end is still translatable and stable; (c) PNPase degrades the small RNA37; (d) the processed pnp mRNA with a single‐stranded 5′‐end is translationally repressed by CsrA and is functionally inactivated by a first RNase E cut within the pnp ORF; (e) upon RNase E cleavage, rapid degradation of the pnp mRNA ensues.
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RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Turnover and Surveillance > Regulation of RNA Stability

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