Genomes and Genes
Summary: An enzyme of the transferase class that catalyzes the reaction RNA(n+1) and orthophosphate to yield RNA(n) and a nucleoside diphosphate, or the reverse reaction. ADP, IDP, GDP, UDP, and CDP can act as donors in the latter case. (From Dorland, 27th ed) EC 126.96.36.199.
- Briani F, Curti S, Rossi F, Carzaniga T, Mauri P, Dehò G. Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli. RNA. 2008;14:2417-29 pubmed publisher..It thus appears that a single mRNA species may be differentially targeted to either decay or PNPase-dependent stabilization, thus preventing its depletion in conditions of fast turnover. ..
- Blum E, Carpousis A, Higgins C. Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro. J Biol Chem. 1999;274:4009-16 pubmed..The inaccessibility of 3'-oligo(U) sequences is likely to have a role in stabilization of RNA molecules generated by Rho-independent terminators...
- Cardenas P, Carrasco B, Sanchez H, Deikus G, Bechhofer D, Alonso J. Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair. Nucleic Acids Res. 2009;37:4157-69 pubmed publisher..Our data suggest that PNPase is involved in various nucleic acid metabolic pathways, and its limited ssDNA exonuclease activity plays an important role in RecA-dependent and RecA-independent repair pathways. ..
- Morita T, Kawamoto H, Mizota T, Inada T, Aiba H. Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Mol Microbiol. 2004;54:1063-75 pubmed..In addition, we show that PNPase and RhlB within the degradosome cooperate to eliminate short degradation intermediates of ptsG mRNA. ..
- Ow M, Liu Q, Kushner S. Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Mol Microbiol. 2000;38:854-66 pubmed..Taken together, these data suggest that the inviability associated with inactivation of RNase E is not related to defects in either mRNA decay or rRNA processing. ..
- Donovan W, Kushner S. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1986;83:120-4 pubmed..In contrast, single-mutant and wild-type control strains grew normally at the nonpermissive temperature and did not accumulate mRNA. No significant changes in rRNA patterns were observed in any of the strains. ..
- Gao J, Lee K, Zhao M, Qiu J, Zhan X, Saxena A, et al. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol Microbiol. 2006;61:394-406 pubmed..coli. ..
- Kido M, Yamanaka K, Mitani T, Niki H, Ogura T, Hiraga S. RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J Bacteriol. 1996;178:3917-25 pubmed..RNase E and PNPase of the multiprotein complex presumably cooperate for effective processing and turnover of specific substrates, such as mRNAs and other RNAs in vivo. ..
- Fernández Ramírez F, Bermudez Cruz R, Montañez C. Nucleic acid and protein factors involved in Escherichia coli polynucleotide phosphorylase function on RNA. Biochimie. 2010;92:445-54 pubmed publisher..Finally, we propose a mechanism of PNPase interactions and discuss their implications in PNPase function. ..
- Piwowarski J, Grzechnik P, Dziembowski A, Dmochowska A, Minczuk M, Stepien P. Human polynucleotide phosphorylase, hPNPase, is localized in mitochondria. J Mol Biol. 2003;329:853-7 pubmed..Here, we demonstrate that the hPNPase is localized in mitochondria. Our finding suggests the involvement of mitochondrial RNA metabolism in cellular senescence. ..
- Le Derout J, Folichon M, Briani F, Deh G, R gnier P, Hajnsdorf E. Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs. Nucleic Acids Res. 2003;31:4017-23 pubmed..Our data led us to the conclusion that Hfq is involved in the recognition of 3' RNA extremities by PAP I...
- Marcaida M, DePristo M, Chandran V, Carpousis A, Luisi B. The RNA degradosome: life in the fast lane of adaptive molecular evolution. Trends Biochem Sci. 2006;31:359-65 pubmed
- Barnett T, Bugrysheva J, Scott J. Role of mRNA stability in growth phase regulation of gene expression in the group A streptococcus. J Bacteriol. 2007;189:1866-73 pubmed..It is possible that PNPase activity is limited in stationary phase, allowing persistence of these important virulence factor transcripts at this phase of growth. ..
- Lin Chao S, Chiou N, Schuster G. The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines. J Biomed Sci. 2007;14:523-32 pubmed..Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes that notably include RNA helicase. ..
- Yamanaka K, Inouye M. Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli. J Bacteriol. 2001;183:2808-16 pubmed
- Roux C, Demuth J, Dunman P. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. J Bacteriol. 2011;193:5520-6 pubmed publisher..Results also revealed that the recently recognized RNase RnpA interacts with the S. aureus degradosome and that this interaction is conserved in other Gram-positive organisms. ..
- Bechhofer D, Wang W. Decay of ermC mRNA in a polynucleotide phosphorylase mutant of Bacillus subtilis. J Bacteriol. 1998;180:5968-77 pubmed..However, it was shown that even PNPase activity could be blocked in vivo at a particular RNA structure. ..
- R gnier P, Grunberg Manago M, Portier C. Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1. J Biol Chem. 1987;262:63-8 pubmed..The possibility that this 69-amino-acid stretch constitutes the polynucleotide binding domain of polynucleotide phosphorylase is discussed...
- Mattiacio J, Read L. Evidence for a degradosome-like complex in the mitochondria of Trypanosoma brucei. FEBS Lett. 2009;583:2333-8 pubmed publisher..This is the first report of a mitochondrial degradosome-like complex outside of yeast. Our data indicate an early evolutionary origin for the mitochondrial SUV3/DSS-1 containing complex. ..
- Prévost K, Desnoyers G, Jacques J, Lavoie F, Massé E. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev. 2011;25:385-96 pubmed publisher..Thus, beyond translation initiation block, sRNA-induced mRNA cleavage requires several unexpected steps, many of which are determined by structural features of the target mRNA. ..
- Nagaike T, Suzuki T, Katoh T, Ueda T. Human mitochondrial mRNAs are stabilized with polyadenylation regulated by mitochondria-specific poly(A) polymerase and polynucleotide phosphorylase. J Biol Chem. 2005;280:19721-7 pubmed..These results demonstrate that the poly(A) length of human mt mRNAs is controlled by polyadenylation by hmtPAP and deadenylation by hPNPase, and polyadenylation is required for the stability of mt mRNAs. ..
- Deikus G, Bechhofer D. Initiation of decay of Bacillus subtilis trp leader RNA. J Biol Chem. 2007;282:20238-44 pubmed..Mutagenesis of nucleotides at the cleavage site abolished processing and resulted in a 4-fold increase in trp leader RNA half-life. This is the first mapping of a decay-initiating endonuclease cleavage site on a native B. subtilis RNA. ..
- Chujo T, Ohira T, Sakaguchi Y, Goshima N, Nomura N, Nagao A, et al. LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria. Nucleic Acids Res. 2012;40:8033-47 pubmed publisher..Moreover, LRPPRC promoted the polyadenylation of mRNAs mediated by mitochondrial poly(A) polymerase (MTPAP) in vitro. These findings provide a framework for understanding the molecular mechanism of mRNA metabolism in human mitochondria. ..
- Luttinger A, Hahn J, Dubnau D. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol Microbiol. 1996;19:343-56 pubmed..This is the first evidence of post-transcriptional effects on the development of competence in B. subtilis. ..
- Py B, Higgins C, Krisch H, Carpousis A. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 1996;381:169-72 pubmed..These results suggest that RhlB acts by unwinding RNA structures that impede the processive activity of PNPase. RhlB is thus an important enzyme in mRNA turnover. ..
- Vanzo N, Li Y, Py B, Blum E, Higgins C, Raynal L, et al. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 1998;12:2770-81 pubmed
- Matus Ortega M, Regonesi M, Piña Escobedo A, Tortora P, Dehò G, Garcia Mena J. The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature. Biochim Biophys Acta. 2007;1769:194-203 pubmed
- Chandran V, Poljak L, Vanzo N, Leroy A, Miguel R, Fernandez Recio J, et al. Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. J Mol Biol. 2007;367:113-32 pubmed
- Arraiano C, Yancey S, Kushner S. Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J Bacteriol. 1988;170:4625-33 pubmed..A new method for high-resolution Northern (RNA) analysis showed that the trxA and cat mRNAs are degraded into discrete fragments which are significantly stabilized only in the triple mutant. A model for mRNA turnover is discussed. ..
- Nurmohamed S, Vaidialingam B, Callaghan A, Luisi B. Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. J Mol Biol. 2009;389:17-33 pubmed publisher..We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome. ..
- Nurmohamed S, Vincent H, Titman C, Chandran V, Pears M, Du D, et al. Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. J Biol Chem. 2011;286:14315-23 pubmed publisher..This communication appears to be part of a feedback network that may contribute to global regulation of metabolism and cellular energy efficiency. ..
- Bermúdez Cruz R, Garcia Mena J, Montañez C. Polynucleotide phosphorylase binds to ssRNA with same affinity as to ssDNA. Biochimie. 2002;84:321-8 pubmedPolynucleotide phosphorylase (PNPase, polyribonucleotide nucleotidyltransferase, EC 188.8.131.52) is a multifunctional protein, with a 3'-5' processive exoribonuclease, a Pi exchange, an RNA polymerase and an autoregulatory activity...
- Andrade J, Arraiano C. PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA. 2008;14:543-51 pubmed publisher..RybB was also destabilized by PNPase. This work highlights a new role for PNPase in the degradation of small noncoding RNAs and opens the way to evaluate striking similarities between bacteria and eukaryotes. ..
- Rainey R, Glavin J, Chen H, French S, Teitell M, Koehler C. A new function in translocation for the mitochondrial i-AAA protease Yme1: import of polynucleotide phosphorylase into the intermembrane space. Mol Cell Biol. 2006;26:8488-97 pubmed..Furthermore, Yme1 has a new function in protein translocation, indicating that the intermembrane space harbors diverse pathways for protein translocation. ..
- Dziembowski A, Malewicz M, Minczuk M, Golik P, Dmochowska A, Stepien P. The yeast nuclear gene DSS1, which codes for a putative RNase II, is necessary for the function of the mitochondrial degradosome in processing and turnover of RNA. Mol Gen Genet. 1998;260:108-14 pubmed..In addition our studies exclude any role for the NUC1 nuclease in these phenomena. ..
- Oussenko I, Abe T, Ujiie H, Muto A, Bechhofer D. Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol. 2005;187:2758-67 pubmed..A threefold increase in the level of peptide tagging was observed in the PNPase-deficient strain, and selective pressure for increased tmRNA activity was indicated by the emergence of mutant strains with elevated tmRNA transcription. ..
- Beran R, Simons R. Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation. Mol Microbiol. 2001;39:112-25 pubmed..Together with other evidence, these results suggest that mRNA is generally stabilized upon a shift to cold temperatures, but that a CSR mRNA-specific decay process is initiated during adaptation. ..
- Leszczyniecka M, Kang D, Sarkar D, Su Z, Holmes M, Valerie K, et al. Identification and cloning of human polynucleotide phosphorylase, hPNPase old-35, in the context of terminal differentiation and cellular senescence. Proc Natl Acad Sci U S A. 2002;99:16636-41 pubmed
- Del Favero M, Mazzantini E, Briani F, Zangrossi S, Tortora P, Dehò G. Regulation of Escherichia coli polynucleotide phosphorylase by ATP. J Biol Chem. 2008;283:27355-9 pubmed publisher..These findings connect RNA turnover with the energy charge of the cell and highlight unforeseen metabolic roles of PNPase. ..
- Cheng Z, Zuo Y, Li Z, Rudd K, Deutscher M. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J Biol Chem. 1998;273:14077-80 pubmed..The identification of the vacB gene product as RNase R should aid in understanding how the virulence phenotype in enterobacteria is expressed and regulated. On the basis of this information we propose that vacB be renamed rnr...
- Goverde R, Huis in t Veld J, Kusters J, Mooi F. The psychrotrophic bacterium Yersinia enterocolitica requires expression of pnp, the gene for polynucleotide phosphorylase, for growth at low temperature (5 degrees C). Mol Microbiol. 1998;28:555-69 pubmed..33 kbp region upstream of pnp harboured a cold-inducible promoter. A putative cold shock promoter motif (ATTGG) was observed in this region...
- Coburn G, Miao X, Briant D, Mackie G. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase. Genes Dev. 1999;13:2594-603 pubmed..A model for degradosome-mediated degradation of structured RNA is presented with its implications for mRNA decay in Escherichia coli...
- Symmons M, Jones G, Luisi B. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure. 2000;8:1215-26 pubmed..A possible function of the trimer channel is as a contribution to both the processivity of degradation and the regulation of PNPase action by RNA structural elements...
- Das S, Bhutia S, Sokhi U, Dash R, Azab B, Sarkar D, et al. Human polynucleotide phosphorylase (hPNPase(old-35)): an evolutionary conserved gene with an expanding repertoire of RNA degradation functions. Oncogene. 2011;30:1733-43 pubmed publisher..In these contexts, targeted overexpression of hPNPase(old-35) represents a novel strategy to selectively downregulate RNA expression and consequently intervene in a variety of pathophysiological conditions. ..
- Callaghan A, Grossmann J, Redko Y, Ilag L, Moncrieffe M, Symmons M, et al. Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain. Biochemistry. 2003;42:13848-55 pubmed..These observations have implications for the structure and function of the RNase E/RNase G ribonuclease family and for the assembly of the E. coli RNA degradosome, in which RNase E is the central component. ..
- Khemici V, Carpousis A. The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol Microbiol. 2004;51:777-90 pubmed
- Leszczyniecka M, DeSalle R, Kang D, Fisher P. The origin of polynucleotide phosphorylase domains. Mol Phylogenet Evol. 2004;31:123-30 pubmed..This result suggests that RPH experienced different evolutionary divergence patterns than the PNPase domains, consistent with the linked nature of the two PNPase domains. ..
- Morita T, Maki K, Aiba H. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 2005;19:2176-86 pubmed..The formation of ribonucleoprotein complexes containing RNases could be a general way by which small RNAs destabilize target mRNAs in both prokaryotes and eukaryotes. ..
- Thiele I, Fleming R, Bordbar A, Schellenberger J, Palsson B. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophys J. 2010;98:2072-81 pubmed publisher..These reactions contribute significant variance among AOS. These results show that constraint-based modeling can be applied to gain insight into the systemic properties of E. coli's transcriptional and translational machinery. ..
- Palanisamy S, Fletcher C, Tanjung L, Katz M, Cheetham B. Deletion of the C-terminus of polynucleotide phosphorylase increases twitching motility, a virulence characteristic of the anaerobic bacterial pathogen Dichelobacter nodosus. FEMS Microbiol Lett. 2010;302:39-45 pubmed publisher..Reconstruction of the pnpA gene in two mutant benign strains reduced twitching motility to the parental level. These results support the hypothesis that PNPase is a virulence repressor in benign strains of D. nodosus...
- Khemici V, Poljak L, Toesca I, Carpousis A. Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Proc Natl Acad Sci U S A. 2005;102:6913-8 pubmed..The possible physiological role of an RhlB-RNase E pathway and the mechanisms by which RhlB could facilitate RNase E cleavage are discussed. ..
- Worrall J, Górna M, Crump N, Phillips L, Tuck A, Price A, et al. Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. J Mol Biol. 2008;382:870-83 pubmed publisher..We discuss the implications for the regulation of RNA degradosome function in vivo. ..