2.7.7.8: polyribonucleotide nucleotidyltransferase
This is an abbreviated version!
For detailed information about polyribonucleotide nucleotidyltransferase, go to the full flat file.
Word Map on EC 2.7.7.8
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2.7.7.8
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rnase
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exoribonuclease
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polya
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ribonuclease
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polymerization
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polyadenylation
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phosphorolysis
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degradosome
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helicase
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exonuclease
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exonucleolytic
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stem-loop
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luteus
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micrococcus
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5'-diphosphate
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rna-binding
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kh
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hfq
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oligoribonucleotides
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rna-degrading
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heteropolymeric
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antibioticus
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dead-box
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lysodeikticus
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primer-independent
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synthesis
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molecular biology
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medicine
- 2.7.7.8
- rnase
- exoribonuclease
- polya
- ribonuclease
- polymerization
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polyadenylation
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phosphorolysis
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degradosome
- helicase
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exonuclease
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exonucleolytic
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stem-loop
- luteus
- micrococcus
- 5'-diphosphate
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rna-binding
- kh
- hfq
- oligoribonucleotides
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rna-degrading
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heteropolymeric
- antibioticus
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dead-box
- lysodeikticus
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primer-independent
- synthesis
- molecular biology
- medicine
Reaction
Synonyms
AtcpPNPase, AtmtPNPase, chloroplast PNPase, cpPNPase, hPNPase(old-35), hPNPaseold-35, nucleoside diphosphate:polynucleotidyl transferase, nucleotidyltransferase, polyribonucleotide, PNP, PNPase, PNPT1, polynucleotide phosphorylase, polyribonucleotide phosphorylase, RNase PH
ECTree
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General Information
General Information on EC 2.7.7.8 - polyribonucleotide nucleotidyltransferase
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evolution
malfunction
metabolism
physiological function
additional information
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human polynucleotide phosphorylase is an evolutionary conserved RNA-processing enzyme. PNPase contains five motifs that are conspicuously preserved through evolution extending from prokaryotes and plants to mammals. Although hPNPase structurally and biochemically resembles PNPase of other species, overexpression and inhibition studies reveal that hPNPase has evolved to serve more specialized and diversified functions in humans
evolution
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polynucleotide phosphorylase is a conserved, widely distributed phosphorolytic 3'-5' exoribonuclease
evolution
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two domains, both resembling closely the phosphorolytic exoribonuclease RNase PH, EC 27.7.56, almost certainly have originated from duplication and fusion of an ancestral gene. While the C-terminal RNase PH-like domain catalyses phosphorolytic attack of RNA, the N-terminal domain has lost this capacity. Instead, it contributes to the ring-like quaternary structure of the trimeric PNPase assembly
evolution
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two domains, both resembling closely the phosphorolytic exoribonuclease RNase PH, EC 27.7.56, almost certainly have originated from duplication and fusion of an ancestral gene. While the C-terminal RNase PH-like domain catalyses phosphorolytic attack of RNA, the N-terminal domain has lost this capacity. Instead, it contributes to the ring-like quaternary structure of the trimeric PNPase assembly
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PNPase-deficient mutant is hypersensitive to oxidative challenges
malfunction
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deletion of the pnp gene, encoding polynucleotide phosphorylase, results in increased biofilm formation in Escherichia coli
malfunction
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enzyme depletion decreases splicing efficiency and inhibits intron degradation, effects on intron metabolism, overview. In mutants lacking cpPNPase activity, unusual RNA patterns occur, intron-containing fragments also accumulate in mutants. Mutants show gene-dependent and intermediate RNA phenotypes, suggesting that reduced enzyme activity differentially affects chloroplast transcripts
malfunction
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in a liver mitochondria from a liver-specific PNPase knockout mouse model, the decrease in functional electron transport chain complexes is responsible for decreased respiration. Liver mitochondria from liver-specific knockout mice display disordered circular and smooth inner membrane criste, similar to mitochondria having impaired components of oxidative phosphorylation pathways. Citrate synthase activity, routinely used as a marker of aerobic capacity, also decreases in the liver of PNPase knockout mice compared with the wild-type mice
malfunction
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inhibition of the enzyme by shRNA or stable overexpression of miR-221 protects melanoma cells from IFN-beta-mediated growth inhibition
malfunction
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loss-of-function mutations in pnp result in a decreased stability of several sRNAs including RyhB, SgrS, and CyaR and also decrease both the negative and positive regulation by sRNAs. The defect in stability of CyaR and in negative and positive regulation are suppressed by deletion mutations in RNase E. Lack of sRNA-mediated regulation in the absence of an active form of PNPase is due to the rapid turnover of sRNA resulting from an increase in RNase E activity and/or an increase in access of other ribonucleases to sRNAs. The defect in sRNA regulation caused by the pnp mutations is independent of Hfq. While Hfq does not appear to be limiting, it seems possible that lack of PNPase leads to inactivation of Hfq
malfunction
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spontaneous mutations resulting from replication errors, which are normally repaired by the mismatch repair system, are sharply reduced in a polynucleotide phosphorylase-deficient Escherichia coli strain
malfunction
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the inactivation of the pnp gene reduces significantly the ability of Campylobacter jejuni to adhere and to invade Ht-29 cells, the mutant strain exhibits a decrease in swimming ability and chick colonization, 81-176 phenotype, overview. The pnp mutation do not induce profound proteomic changes suggesting that other ribonucleases in the organism might ensure this biological function in the absence of PNPase
malfunction
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loss-of-function mutations in pnp result in a decreased stability of several sRNAs including RyhB, SgrS, and CyaR and also decrease both the negative and positive regulation by sRNAs. The defect in stability of CyaR and in negative and positive regulation are suppressed by deletion mutations in RNase E. Lack of sRNA-mediated regulation in the absence of an active form of PNPase is due to the rapid turnover of sRNA resulting from an increase in RNase E activity and/or an increase in access of other ribonucleases to sRNAs. The defect in sRNA regulation caused by the pnp mutations is independent of Hfq. While Hfq does not appear to be limiting, it seems possible that lack of PNPase leads to inactivation of Hfq
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malfunction
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PNPase-deficient mutant is hypersensitive to oxidative challenges
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malfunction
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deletion of the pnp gene, encoding polynucleotide phosphorylase, results in increased biofilm formation in Escherichia coli
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malfunction
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enzyme depletion decreases splicing efficiency and inhibits intron degradation, effects on intron metabolism, overview. In mutants lacking cpPNPase activity, unusual RNA patterns occur, intron-containing fragments also accumulate in mutants. Mutants show gene-dependent and intermediate RNA phenotypes, suggesting that reduced enzyme activity differentially affects chloroplast transcripts
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PNPase, together with the endonuclease RNase E, the DEAD-box RNA helicase RhlB, and enolase, constitutes the RNA degradosome, a multiprotein machine devoted to RNA degradation
metabolism
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the enzyme is involved in RNA degradation and/turnover, major processes controlling RNA levels and important regulators of physiological and pathological processes
metabolism
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the Krebs cycle metabolite citrate affects the activity of Escherichia coli polynucleotide phosphorylase (PNPase) and, conversely, that cellular metabolism is affected widely by PNPase activity, a PNPase-mediated response to citrate, and PNPase deletion broadly impacts on the metabolome and on global gene expression, detailed overview
metabolism
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the Krebs cycle metabolite citrate affects the activity of Escherichia coli polynucleotide phosphorylase (PNPase) and, conversely, that cellular metabolism is affected widely by PNPase activity, a PNPase-mediated response to citrate, and PNPase deletion broadly impacts on the metabolome and on global gene expression, detailed overview
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metabolism
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PNPase, together with the endonuclease RNase E, the DEAD-box RNA helicase RhlB, and enolase, constitutes the RNA degradosome, a multiprotein machine devoted to RNA degradation
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Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair
physiological function
PNPase is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors
physiological function
PNPase is a virulence repressor in benign strains of Dichelobacter nodosus
physiological function
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PNPase may be solely responsible for chloroplast polyadenylation activity
physiological function
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PNPase may be solely responsible for chloroplast polyadenylation activity
physiological function
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PNPase plays a role of in low-temperature survival of Campylobacter jejuni
physiological function
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PNPase primarily functions in exonucleolytic degradation of RNA in the 3'->5' direction, PNPase also functions in minimizing oxidized RNA in vivo
physiological function
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PNPase regulates chloroplast transcript accumulation in response to phosphorus starvation, the activity of the chloroplast PNPase is involved in plant acclimation to phosphorus availability and may help maintain an appropriate balance of phosphorus metabolites even under normal growth conditions
physiological function
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hPNPaseold-35 regulates the expression of specific miRNAs, importance of hPNPaseold-35 induction and miR-221 downregulation in mediating IFN-beta action, mechanism of miRNA regulation involving selective enzymatic degradation, overview
physiological function
human polynucleotide phosphorylase is a 3'-to-5' exoribonuclease that degrades specific mRNA and miRNA, and imports RNA into mitochondria, and thus regulates diverse physiological processes, including cellular senescence and homeostasis
physiological function
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metabolite-bound PNPase structure and evidence for an allosteric pocket, overview
physiological function
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pivotal role of PNPase in mitochondrial morphogenesis and respiration in vivo
physiological function
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polynucleotide phosphorylase is an exoribonuclease that cleaves single-stranded RNA substrates with 3' -5' directionality and processive behaviour
physiological function
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polynucleotide phosphorylase is an RNA processing enzyme and a component of the RNA degradosome. It plays an important role in RNA processing and turnover, being implicated in RNA degradation and in polymerization of heteropolymeric tails at the 3'-end of mRNA. PNPase is necessary to maintain bacterial cells in the planktonic mode through downregulation of pgaABCD expression and poly-N-acetylglucosamine production. But the pnp gene is not essential. Negative regulation of the poly-N-acetylglucosamine biosynthetic operon pgaABCD by PNPase
physiological function
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polynucleotide phosphorylase is an RNA-processing enzyme with expanding roles in regulating cellular physiology. By executing exonuclease activity PNPase specifically degrades mature miRNAs, schematic model of microRNA biogenesis and stability, overview. The enzyme might have an essential role in senescence- and differentiation-associated growth inhibition, involvement of hPNPase in producing pathological changes associated with aging by generating pro-inflammatory cytokines via reactive oxygen species and NF-kappaB, growth inhibition in different cancer cells and its molecular mechanism, overview. Direct involvement of PNPase in regulating specific cytosolic RNA import into the mitochondrial matrix, independently of its RNA-processing function
physiological function
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polynucleotide phosphorylase plays a central role in RNA degradation, generating a pool of ribonucleoside diphosphates that can be converted to deoxyribonucleoside diphosphates by ribonucleotide reductase
physiological function
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the chloroplastidic enzyme has a major role in maturing mRNA and rRNA 3'-ends, but also participates in RNA degradation through exonucleolytic digestion and polyadenylation.Cchloroplast PNPase and a poly(A) polymerase share the polymerization role in wild-type plants. Chloroplast PNPase appears to be required for a degradation step following endonucleolytic cleavage of the excised lariat. The enzyme functions depend absolutely on the catalytic site within the second duplicated RNase PH domain, and appear to be modulated by the first RNase PH domain, but both PNPase domains contribute to chloroplast rRNA and mRNA processing, overview
physiological function
deletion of the gene encoding PNPase leads to hyperaggregation and increased adhesion to epithelial cells. The aggregation induced is dependent on pili and mediated by excessive pilus bundling. PNPase expression is induced following bacterial attachment to human cells. Deletion of PNPase leads to global transcriptional changes and the differential regulation of 469 genes. PNPase is required for full virulence in an in vivo model of N. meningitidis infection
physiological function
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in vitro, enzyme forms a ternary complex comprised of PNPase, chaperine Hfq, and sRNA and PNPase and Hfq may also form a ribonucleoprotein complex in the cell. In in vitro studies, PNPase readily degrades sRNAs in the absence of Hfq, but binds and is unable to degrade sRNAs in its presence
physiological function
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mutations in PNPase residues predicted to be involved in RNase Y binding show a loss of PNPase-RNase Y interaction. For the two mRNAs investigated, disruption of the PNPase-RNase Y interaction does not appear to affect mRNA turnover
physiological function
PNPase discriminates RNA versus DNA during the 3' phosphorolysis reaction. A kinetic block to 3' phosphorolysis of a DNA tract within an RNA polynucleotide is exerted when resection has progressed to the point that a 3' monoribonucleotide flanks the impeding DNA segment. The position of the pause one nucleotide upstream of the first deoxynucleotide encountered is independent of DNA tract length. The duration of the pause is affected by DNA tract length, being transient for a single deoxynucleotide and durable when two or more consecutive deoxynucleotides are encountered
physiological function
PNPase forms a complex with RNase E. An extremely conserved nonapeptide (RRRRRRSSA) located near the very end of RNase E, serves as the PNPase recognition site in both the filamentous cyanobacterium Anabaena sp. PCC7120 and the unicellular cyanobacterium Synechocystis sp. PCC6803
physiological function
PNPase forms a complex with RNase E. An extremely conserved nonapeptide (RRRRRRSSA) located near the very end of RNase E, serves as the PNPase recognition site in both the filamentous cyanobacterium Anabaena sp. PCC7120 and the unicellular cyanobacterium Synechocystis sp. PCC6803
physiological function
the cvfA-deletion mutant phenotype showing decreased agr expression and hemolysin production, is suppressed by disrupting pnpA-encoding PNPase. Loss of the 3'- to 5'-exonuclease activity is required for suppression. CvfA protein hydrolyzes a 2',3'-cyclic phosphodiester bond at the RNA 3' terminus, producing RNA with a 3'-phosphate. Purified PNPase efficiently degrades RNA with 2',3'-cyclic phosphate at the 3' terminus (2',3'-cyclic RNA), but it inefficiently degrades 3'-phosphorylated RNA
physiological function
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the KH-S1 domains of PNPase are required for the type III secretion system (T3SS) and bacterial virulence. PNPase shows a pleiotropic role in gene regulation. The RNA level of exsA is decreased in a mutant lacking the KH-S1 domains. The pilus biosynthesis genes are down regulated and the type VI secretion system (T6SS) genes are up regulated in the mutant, which is caused by increased levels of small RNAs, RsmY, and RsmZ. Deletion of the KH-S1 domains does not affect the transcription of RsmY/Z, but increases their stabilities
physiological function
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the Pnp gene is required for Salmonella typhimurium virulence and gastrointestinal colonization of the natural swine host. Following intranasal inoculation, a significant increase in rectal temperature is observed in the pigs inoculated with wild-type Salmonella typhimurium compared to the pigs inoculated with the Pnp mutant. Fecal shedding of the Pnp mutant is significantly reduced during the 7-day study compared to the wild-type strain. Tissue colonization is also significantly reduced in the pigs inoculated with the pnp mutant, including the tonsils, ileocecal lymph nodes, Peyer's Patch region of the ileum, cecum and contents of the cecum
physiological function
compared to the wild type, the production of fengycin in mutant strains lacking PNPase activity has decreased by about 70-40%, and its antifungal activity towards the plant pathogen Botrytis cinerea is hampered
physiological function
in cardiac tissue from human and mouse models of type 2 diabetes mellitus, levels of Argonaute2 protein, associated with cytosolic and mitochondrial miRNAs, are unchanged while PNPase protein expression levels are increased. There an increase in the association between both proteins in the diabetic state
physiological function
mutation of the polynucleotide phosphorylase coding gene pnp increases the bacterial resistance to ciprofloxacin.The expression of pyocin biosynthesis genes is decreased in the pnp mutant. PrtR, a negative regulator of pyocin biosynthesis genes, is upregulated in the pnp mutant. Polynucleotide phosphorylase represses the expression of PrtR on the posttranscriptional level. A fragment containing 43 nucleotides of the 5' untranslated region is involved in the polynucleotide phosphorylase mediated regulation of PrtR
physiological function
mutation of the polynucleotide phosphorylase encoding gene increases bacterial tolerance to aminoglycoside antibiotics. The upregulation of the multidrug efflux pump MexXY genes is responsible for the increased tolerance of the polynucleotide phosphorylase mutant. Polynucleotide phosphorylase controls the translation of the armZ mRNA, which regulates the expression of MexXY through its 59 untranslated region
physiological function
PNPase forms a complex with RNase J1 and RNase J2 without substantially altering either exo-ribonuclease or polyadenylation activity of the enzyme
physiological function
PNPase is a contributor to mitochondrial miRNA import through the transport of miRNA-378, which may regulate bioenergetics during type 2 diabetes mellitus. In cardiac tissue from human and mouse models of type 2 diabetes mellitus, levels of Argonaute2 protein, associated with cytosolic and mitochondrial miRNAs, are unchanged while PNPase protein expression levels are increased. There an increase in the association between both proteins in the diabetic state. miRNA-378 is significantly increased in db/db mice, leading to decrements in ATP6 levels and ATP synthase activity, which is also exhibited when overexpressing PNPase in HL-1 cardiomyocytes
physiological function
polynucleotide phosphorylase and endo-type RNases, RNase E/G and YbeY, are involved in the 3' maturation of 4.5S RNA in Corynebacterium glutamicum. The mature form of 4.5S RNA is inefficiently formed in RNase E/G/polynucleotide phosphorylase mutant cells. Immunoprecipitated Ffh protein of the signal recognition particle contains immature 4.5S RNA in RNase E/G, in polynucleotide phosphorylase and in mutants RNase YbeY mutants
physiological function
polynucleotide phosphorylase and RNase PH interact to support sRNA stability, activity, and base pairing in exponential and stationary growth conditions. They facilitate the stability and regulatory function of the sRNAs RyhB, CyaR, and MicA during exponential growth. Polynucleotide phosphorylase may contribute to pairing between RyhB and its mRNA targets. During stationary growth, each sRNA responds differently to the absence or presence of PNPase and RNase PH. Polynucleotide phosphorylase and RNase PH stabilize only Hfq-bound sRNAs
physiological function
polynucleotide phosphorylase contributes to the degradation of specific short mRNA fragments, the majority of which bind RNA chaperone Hfq and are derived from targets of sRNAs. The mRNA-derived fragments accumulate in the absence of polynucleotide phosphorylase or its exoribonuclease activity and interact with polynucleotide phosphorylase. Mutations in chaperone Hfq or in the seed pairing region of some sRNAs eliminate the requirement of polynucleotide phosphorylase for their stability
physiological function
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polynucleotide phosphorylase enhances both homologous recombination upon P1 transduction and error prone DNA repair of double strand breaks induced by radiomimetic zeocin. Homologous recombination does not require polynucleotide phosphorylasephosphorolytic activity and is modulated by its RNA binding domains whereas error prone DNA repair of zeocin-induced DNA damage is dependent on polynucleotide phosphorylase catalytic activity and cannot be suppressed by overexpression of RNase II. Polynucleotide phosphorylase mutants are more sensitive than the wild-type to zeocin. This phenotype depends on polynucleotide phosphorylasephosphorolytic activity and is suppressed by RNase II
physiological function
polynucleotide phosphorylase is involved in controlling the levels of RNA oxidation marker 8-hydrooxyguanosine in both cytoplasmic and mitochondrial fractions. Expression of exogenous polynucleotide phosphorylase reduces 8-hydrooxyguanosine levels in both cytoplasm and mitochondria. The S1 RNA binding domain is crucial for reducing 8-hydrooxyguanosine in both cytoplasm and mitochondria, while the N-terminal mitochondrial translocation signal is required for 8-hydrooxyguanosine reduction in mitochondria. One of the RPH1 or RPH2 domains is sufficient to reduce 8-hydrooxyguanosine levels in RNA under oxidative stress conditions
physiological function
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compared to the wild type, the production of fengycin in mutant strains lacking PNPase activity has decreased by about 70-40%, and its antifungal activity towards the plant pathogen Botrytis cinerea is hampered
-
physiological function
-
polynucleotide phosphorylase is an exoribonuclease that cleaves single-stranded RNA substrates with 3' -5' directionality and processive behaviour
-
physiological function
-
mutations in PNPase residues predicted to be involved in RNase Y binding show a loss of PNPase-RNase Y interaction. For the two mRNAs investigated, disruption of the PNPase-RNase Y interaction does not appear to affect mRNA turnover
-
physiological function
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PNPase primarily functions in exonucleolytic degradation of RNA in the 3'->5' direction, PNPase also functions in minimizing oxidized RNA in vivo
-
physiological function
-
Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair
-
physiological function
-
deletion of the gene encoding PNPase leads to hyperaggregation and increased adhesion to epithelial cells. The aggregation induced is dependent on pili and mediated by excessive pilus bundling. PNPase expression is induced following bacterial attachment to human cells. Deletion of PNPase leads to global transcriptional changes and the differential regulation of 469 genes. PNPase is required for full virulence in an in vivo model of N. meningitidis infection
-
physiological function
-
PNPase forms a complex with RNase E. An extremely conserved nonapeptide (RRRRRRSSA) located near the very end of RNase E, serves as the PNPase recognition site in both the filamentous cyanobacterium Anabaena sp. PCC7120 and the unicellular cyanobacterium Synechocystis sp. PCC6803
-
physiological function
-
metabolite-bound PNPase structure and evidence for an allosteric pocket, overview
-
physiological function
-
polynucleotide phosphorylase is an RNA processing enzyme and a component of the RNA degradosome. It plays an important role in RNA processing and turnover, being implicated in RNA degradation and in polymerization of heteropolymeric tails at the 3'-end of mRNA. PNPase is necessary to maintain bacterial cells in the planktonic mode through downregulation of pgaABCD expression and poly-N-acetylglucosamine production. But the pnp gene is not essential. Negative regulation of the poly-N-acetylglucosamine biosynthetic operon pgaABCD by PNPase
-
physiological function
-
the chloroplastidic enzyme has a major role in maturing mRNA and rRNA 3'-ends, but also participates in RNA degradation through exonucleolytic digestion and polyadenylation.Cchloroplast PNPase and a poly(A) polymerase share the polymerization role in wild-type plants. Chloroplast PNPase appears to be required for a degradation step following endonucleolytic cleavage of the excised lariat. The enzyme functions depend absolutely on the catalytic site within the second duplicated RNase PH domain, and appear to be modulated by the first RNase PH domain, but both PNPase domains contribute to chloroplast rRNA and mRNA processing, overview
-
physiological function
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PNPase forms a complex with RNase J1 and RNase J2 without substantially altering either exo-ribonuclease or polyadenylation activity of the enzyme
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physiological function
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polynucleotide phosphorylase and endo-type RNases, RNase E/G and YbeY, are involved in the 3' maturation of 4.5S RNA in Corynebacterium glutamicum. The mature form of 4.5S RNA is inefficiently formed in RNase E/G/polynucleotide phosphorylase mutant cells. Immunoprecipitated Ffh protein of the signal recognition particle contains immature 4.5S RNA in RNase E/G, in polynucleotide phosphorylase and in mutants RNase YbeY mutants
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also see for EC 2.7.7.56. RNase PH, EC 2.7.7.8, consists of tandem N-terminal RNase PH-like segments, known as core domains, as well as KH and S1 RNA-binding domains. The conserved residue D625 is located in the catalytic site and functions in phosphorolysis
additional information
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human melanoma cells infected with an adenovirus expressing hPNPaseold-35 and are used for identification of miRNAs differentially and specifically regulated by hPNPaseold-35. Overexpression of miR-221 in HO-1 cells confers resistance to IFN-beta-mediated growth arrest
additional information
the C-terminal S1 domain is not critical for RNA binding, and conversely, the conserved GXXG motif in the KH domain directly participates in RNA binding in hPNPase. The enzyme uses a KH pore to trap a long RNA 3' tail that is further delivered into an RNase PH channel for the degradation process. The three KH domains form a KH pore situated on the top of the hexameric ring-like structure. The KH pore extends the central channel formed by the RNase PH domains and is involved in the binding of RNA substrates, which are further delivered to the active site located within the central channel. Structural RNA with short 3' tails are, on the other hand, transported but not digested by hPNPase. Structural model of hPNPase, overview
additional information
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the C-terminal S1 domain is not critical for RNA binding, and conversely, the conserved GXXG motif in the KH domain directly participates in RNA binding in hPNPase. The enzyme uses a KH pore to trap a long RNA 3' tail that is further delivered into an RNase PH channel for the degradation process. The three KH domains form a KH pore situated on the top of the hexameric ring-like structure. The KH pore extends the central channel formed by the RNase PH domains and is involved in the binding of RNA substrates, which are further delivered to the active site located within the central channel. Structural RNA with short 3' tails are, on the other hand, transported but not digested by hPNPase. Structural model of hPNPase, overview
additional information
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the enzyme has a ring-like, trimeric architecture that creates a central channel where phosphorolytic active sites reside, with asymmetry within the catalytic core of the enzyme. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains. In the RNA-free form, the S1 domains adopt a splayed conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. Structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Access to the PNPase active sites is through the central channel, which can accommodate single-stranded RNA with some structural adjustment of a constricted aperture at the channel entrance, residues and motifs involved in RNA directionality, recognition, and quarternary changes in the core, structure-function-relationship, detailed overview
additional information
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the increase in the rNDP pools generated by polynucleotide phosphorylase degradation of RNA is responsible for the spontaneous mutations observed in an mismatch repair-deficient background, and is also responsible for the observed mutations in the mutT mutator background and those that occur after treatment with 5-bromodeoxyuridine
additional information
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the S1 and KH domains of polynucleotide phosphorylase determine the efficiency of RNA binding and enzyme autoregulation, modeling of the roles of the KH and S1 domains in PNPase-RNA interactions and in substrate binding, overview
additional information
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two conserved catalytic RNase PH regions, a small domain of about 250 amino acid residues involved primarily in the 3' processing of transfer RNA precursors, are present at the N-terminus of the human enzyme. The RNA-binding property of hPNPase is conferred by two C-terminal RNA-binding domains, KH and S1
additional information
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the enzyme has a ring-like, trimeric architecture that creates a central channel where phosphorolytic active sites reside, with asymmetry within the catalytic core of the enzyme. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains. In the RNA-free form, the S1 domains adopt a splayed conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. Structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Access to the PNPase active sites is through the central channel, which can accommodate single-stranded RNA with some structural adjustment of a constricted aperture at the channel entrance, residues and motifs involved in RNA directionality, recognition, and quarternary changes in the core, structure-function-relationship, detailed overview
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additional information
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also see for EC 2.7.7.56. RNase PH, EC 2.7.7.8, consists of tandem N-terminal RNase PH-like segments, known as core domains, as well as KH and S1 RNA-binding domains. The conserved residue D625 is located in the catalytic site and functions in phosphorolysis
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