PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins

Andrade, José M.; Arraiano, Cecília M.

doi:10.1261/rna.683308

Cited by 74 publications

(82 citation statements)

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“…hPNPase old-35 is a 3′, 5′ exoribonuclease that catalyzes the phosphorolysis of RNA, generating nucleoside diphosphates as cleavage products (26). We demonstrated previously that hPNPase old-35 could specifically degrade c-myc mRNA, resulting in growth arrest in human melanoma cells (16). Apart from our study, a number of additional potential substrates for hPNPase old-35 have been identified, including small RNA and noncoding RNA.…”

Section: Discussionmentioning

confidence: 55%

“…Analysis of the expression profile of hPNPase old-35 revealed that it is predominantly a type I IFN-inducible gene and might play an essential role in IFN-induced growth arrest in human melanoma cells by executing its exonuclease activity on c-myc mRNA (12)(13)(14)(15). Apart from c-myc mRNA degradation, hPNPase old-35 is also involved in regulating the levels of several small noncoding RNAs (16). Very recently, Wang et al (17) reported that hPNPase old-35 , along with human mitochondrial SUV 3 (suppressor of Var1 3), degrades dsRNA in the 3′-to-5′ direction.…”

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confidence: 99%

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Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells

Das

Sokhi

Bhutia

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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MicroRNAs (miRNA), small noncoding RNAs, affect a broad range of biological processes, including tumorigenesis, by targeting gene products that directly regulate cell growth. Human polynucleotide phosphorylase (hPNPase old-35 ), a type I IFN-inducible 3′-5′ exoribonuclease, degrades specific mRNAs and small noncoding RNAs. The present study examined the effect of this enzyme on miRNA expression in human melanoma cells. miRNA microarray analysis of human melanoma cells infected with empty adenovirus or with an adenovirus expressing hPNPase old-35 identified miRNAs differentially and specifically regulated by hPNPase old-35 . One of these, miR-221, a regulator of the cyclin-dependent kinase inhibitor p27 kip1 , displayed robust down-regulation with ensuing up-regulation of p27 kip1 by expression of hPNPase old-35 , which also occurred in multiple human melanoma cells upon IFN-β treatment. Using both in vivo immunoprecipitation followed by Northern blotting and RNA degradation assays, we confirm that mature miR-221 is the target of hPNPase old-35 . Inhibition of hPNPase old-35 by shRNA or stable overexpression of miR-221 protected melanoma cells from IFN-β-mediated growth inhibition, accentuating the importance of hPNPase old-35 induction and miR-221 down-regulation in mediating IFN-β action. Moreover, we now uncover a mechanism of miRNA regulation involving selective enzymatic degradation. Targeted overexpression of hPNPase old-35 might provide an effective therapeutic strategy for miR-221-overexpressing and IFN-resistant tumors, such as melanoma.M icroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs that regulate gene expression at the posttranscriptional level and play important roles in a multiplicity of biological functions, including cell differentiation, tumorigenesis, apoptosis, and metabolism (1). miRNA genes are initially transcribed principally by either RNA polymerase II or RNA polymerase III as long primary transcripts, which are further processed by the nuclear RNase Drosha and cytoplasmic RNase Dicer to produce precursor miRNAs and mature miRNAs, respectively (2). miRNAs recognize and bind to partially complementary sites in the 3′ UTRs of target mRNAs, resulting in either translational repression or target degradation (3). The steadystate levels of miRNAs, crucial for its profound impact on a wide array of biological processes (4, 5), are presumably determined by the opposing activities of miRNA biogenesis and degradation. Although the framework of miRNA biogenesis is established, factors involved in miRNA dysregulation remain unknown. Recent work from Ramachandran and Chen (6) documented that an exoribonuclease encoded by small rna degrading nuclease (sdn) gene degrades mature miRNAs in Arabidopsis. Although in human cells the posttranscriptional control of miRNA is poorly defined, it can be hypothesized that enzymes involved in miRNA metabolism evolved from enzymes that process structural and/or catalytic RNAs, a view supported by the fact that a number of known molecules involved...

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Section: Discussionmentioning

confidence: 55%

mentioning

confidence: 99%

Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells

Das

Sokhi

Bhutia

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…36 A major role of PNPase in the turn-over of several small RNAs that control expression of outer membrane proteins was demonstrated in E. coli. 37 In general little is known to date on different levels or activities of RNases or their different organization in protein complexes in different growth phases.…”

Section: Discussionmentioning

confidence: 99%

The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its targetrpoSinE. coliis growth phase dependent

Basineni

Madhugiri²,

Kolmsee³

et al. 2009

RNA Biology

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“…Consequently, this protection of the 3′ end will not only help stabilize the respective RNA (13), but also suggests a pathway for freshly transcribed sRNAs to actively switch off the effects of other, preexisting sRNAs in a rapid way, simply by competing them out from Hfq and exposing them to accelerated degradation. Indeed, Hfq has been found to protect the primary RNA 3′ end of both mRNAs from oligoadenylation by poly(A) polymerase I (5) and sRNAs from degradation mediated by polynucleotide phosphorylase (29).…”

Section: The Free 3′-terminal Hydroxyl Group Is Crucial For the High-mentioning

confidence: 99%

Structural basis for RNA 3′-end recognition by Hfq

Sauer

Weichenrieder

2011

Proc. Natl. Acad. Sci. U.S.A.

192

251

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The homohexameric (L)Sm protein Hfq is a central mediator of small RNA-based gene regulation in bacteria. Hfq recognizes small regulatory RNAs (sRNAs) specifically, despite their structural diversity. This specificity could not be explained by previously described RNA-binding modes of Hfq. Here we present a distinct and preferred mode of Hfq-RNA interaction that involves the direct recognition of a uridine-rich RNA 3′ end. This feature is common in bacterial RNA transcripts as a consequence of Rho-independent transcription termination and hence likely contributes significantly to the general recognition of sRNAs by Hfq. Isothermal titration calorimetry shows nanomolar affinity between Salmonella typhimurium Hfq and a hexauridine substrate. We determined a crystal structure of the complex that reveals a constricted RNA backbone conformation in the proximal RNA-binding site of Hfq, allowing for a direct protein contact of the 3′ hydroxyl group. A free 3′ hydroxyl group is crucial for the high-affinity interaction with Hfq also in the context of a full-length sRNA substrate, RybB. The capacity of Hfq to occupy and sequester the RNA 3′ end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation.RNA chaperone | regulation of translation | RNA degradation | prokaryotes H fq is an abundant and widely conserved RNA-binding protein in bacteria and a major player in the RNA-based regulation of gene expression, such as in the adaptive response to cell stress or in the induction of virulence (1, 2).Hfq was originally identified as a host factor in Escherichia coli for the replication of the Qβ phage (3), where it binds to the C-rich 3′ end of plus-strand viral RNA (4). Subsequently, physiological roles of Hfq were described in the regulation of mRNA translation and in mRNA degradation, where it modulates the processing of RNA 3′ ends (1,(5)(6)(7)(8). The most prominent function of Hfq, however, is its interaction with small regulatory RNAs (sRNAs) that act in trans and that are differentially expressed under various metabolic and environmental conditions (9, 10). They globally regulate gene expression via base-pairing to frequently entire sets of partially complementary mRNAs (11,12). Hfq stabilizes sRNAs in the absence of their targets (13). Hfq was also found to facilitate base-pairing to the mRNAs and help trigger subsequent steps, such as the repression of translation and/or the acceleration of decay, but also mRNA activation (11,14). Despite their structural diversity, the recognition of many sRNAs by Hfq is highly specific and even works across species barriers (15). It is an intriguing question how this selectivity is achieved.Crystal structures reveal that bacterial Hfq adopts an (L)Sm fold and forms homohexameric rings, whereas related (L)Sm proteins [Sm proteins and Sm-like (LSm) proteins] in archaea and eukaryotes are found to form homomeric or heteromeric heptamers, respectively (16). Two distinct RNA-binding sites have been described on opposite f...

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PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins

Cited by 74 publications

References 46 publications

Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells

Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells

The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its targetrpoSinE. coliis growth phase dependent

Structural basis for RNA 3′-end recognition by Hfq

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