Genomes and Genes
Summary: An enzyme that catalyzes the synthesis of polyadenylic acid from ATP. May be due to the action of RNA polymerase (EC 22.214.171.124) or polynucleotide adenylyltransferase (EC 126.96.36.199). EC 188.8.131.52.
- Mohanty B, Maples V, Kushner S. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol Microbiol. 2004;54:905-20 pubmed..Analysis of mRNA half-lives in hfq, deltapcnB and hfq deltapcnB mutants suggests that Hfq and PAP I function in the same mRNA decay pathway. ..
- Vanacova S, Wolf J, Martin G, Blank D, Dettwiler S, Friedlein A, et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 2005;3:e189 pubmed..This polyadenylation-mediated RNA surveillance resembles the role of polyadenylation in bacterial RNA turnover. ..
- Milligan L, Torchet C, Allmang C, Shipman T, Tollervey D. A nuclear surveillance pathway for mRNAs with defective polyadenylation. Mol Cell Biol. 2005;25:9996-10004 pubmed..In wild-type strains, assembly of the cleavage and polyadenylation complex might be suboptimal at cryptic polyadenylation sites, causing slowed polyadenylation. ..
- Söderbom F, Binnie U, Masters M, Wagner E. Regulation of plasmid R1 replication: PcnB and RNase E expedite the decay of the antisense RNA, CopA. Mol Microbiol. 1997;26:493-504 pubmed..We also find that, as predicted, under conditions in which CopA synthesis is unaffected, pcnB mutation reduces RepA translation and increases CopA stability to the same extent. ..
- Zhao W, Manley J. Complex alternative RNA processing generates an unexpected diversity of poly(A) polymerase isoforms. Mol Cell Biol. 1996;16:2378-86 pubmed..Purified recombinant baculovirus-expressed PAPs were tested in several in vitro assays, and the short forms were found to be inactive. We discuss the possible significance of this complex expression pattern. ..
- Grzechnik P, Kufel J. Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol Cell. 2008;32:247-58 pubmed publisher..We propose a model in which polyadenylation of pre-snoRNAs is a key event linking their transcription termination, 3' end processing, and degradation. ..
- Kuhn U, Gündel M, Knoth A, Kerwitz Y, Rüdel S, Wahle E. Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor. J Biol Chem. 2009;284:22803-14 pubmed publisher..PABPN1 measures the length of the tail and is responsible for disrupting the CPSF-poly(A) polymerase interaction. ..
- Xu F, Lin Chao S, Cohen S. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proc Natl Acad Sci U S A. 1993;90:6756-60 pubmed..Accumulation of antisense RNAI decay products in pcnB mutants potentially explains the reduced copy number of ColE1-type plasmids seen in the mutated bacteria. ..
- Rammelt C, Bilen B, Zavolan M, Keller W. PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA. 2011;17:1737-46 pubmed publisher..In contrast to the yeast protein, the C terminus of PAPD5 contains a stretch of basic amino acids that is involved in binding the RNA substrate. ..
- Viegas S, Pfeiffer V, Sittka A, Silva I, Vogel J, Arraiano C. Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res. 2007;35:7651-64 pubmed..Taken together, the results of this study provide initial insight into the mechanisms of sRNA decay in Salmonella, and indicate specific contributions of the RNA decay machinery components to the turnover of individual sRNAs. ..
- Ziolkowska K, Derreumaux P, Folichon M, Pellegrini O, Regnier P, Boni I, et al. Hfq variant with altered RNA binding functions. Nucleic Acids Res. 2006;34:709-20 pubmed
- Reichenbach B, Maes A, Kalamorz F, Hajnsdorf E, Görke B. The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli. Nucleic Acids Res. 2008;36:2570-80 pubmed publisher..In pcnB mutants, GlmY accumulates and induces glmS expression by stabilizing full-length GlmZ. Hence, the data reveal a regulatory cascade composed of two sRNAs, which responds to GlcN-6-P and is controlled by polyadenylation. ..
- Barnard D, Ryan K, Manley J, Richter J. Symplekin and xGLD-2 are required for CPEB-mediated cytoplasmic polyadenylation. Cell. 2004;119:641-51 pubmed..The identification of these factors has broad implications for biological process that employ polyadenylation-regulated translation, such as gametogenesis, cell cycle progression, and synaptic plasticity. ..
- Preker P, Lingner J, Minvielle Sebastia L, Keller W. The FIP1 gene encodes a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. Cell. 1995;81:379-89 pubmed..We propose a model in which PF I tethers PAP1 to CF I, thereby conferring specificity to poly(A) polymerase for pre-mRNA substrates. ..
- Ohnacker M, Barabino S, Preker P, Keller W. The WD-repeat protein pfs2p bridges two essential factors within the yeast pre-mRNA 3'-end-processing complex. EMBO J. 2000;19:37-47 pubmed..These results show that Pfs2p plays an essential role in 3'-end formation by bridging different processing factors and thereby promoting the assembly of the processing complex. ..
- Hajnsdorf E, Regnier P. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A. 2000;97:1501-5 pubmed..The similar properties of Hfq and the PABPII poly(A) binding protein, which stimulates poly(A) tail elongation in mammals, indicates that similar mechanisms control poly(A) tail synthesis in prokaryotes and eukaryotes. ..
- Preker P, Ohnacker M, Minvielle Sebastia L, Keller W. A multisubunit 3' end processing factor from yeast containing poly(A) polymerase and homologues of the subunits of mammalian cleavage and polyadenylation specificity factor. EMBO J. 1997;16:4727-37 pubmed..PF I also appears to be functionally related to CPSF, as it polyadenylates a substrate RNA more efficiently than Pap1p alone. Possibly, the observed interaction of the complex with RNA tethers Pap1p to its substrate. ..
- Minvielle Sebastia L, Preker P, Wiederkehr T, Strahm Y, Keller W. The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3'-end formation. Proc Natl Acad Sci U S A. 1997;94:7897-902 pubmed..Our data support the notion that Pab1p is involved in the length control of the poly(A) tails of yeast mRNAs and define a new essential function for Pab1p in the formation of mature mRNAs. ..
- Wyers F, Rougemaille M, Badis G, Rousselle J, Dufour M, Boulay J, et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell. 2005;121:725-37 pubmed..Our data strongly support the existence of a posttranscriptional quality control mechanism limiting inappropriate expression of genetic information. ..
- Gebauer F, Richter J. Cloning and characterization of a Xenopus poly(A) polymerase. Mol Cell Biol. 1995;15:1422-30 pubmed..These data suggest that the PAP described here could participate in cytoplasmic polyadenylation during Xenopus oocyte maturation. ..
- Martin G, Keller W. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 1996;15:2593-603 pubmed..This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor. ..
- Bienroth S, Keller W, Wahle E. Assembly of a processive messenger RNA polyadenylation complex. EMBO J. 1993;12:585-94 pubmed..Only the complex formed from all three proteins is competent for the processive synthesis of a full-length poly(A) tail. ..
- Joanny G, Le Derout J, Brechemier Baey D, Labas V, Vinh J, Regnier P, et al. Polyadenylation of a functional mRNA controls gene expression in Escherichia coli. Nucleic Acids Res. 2007;35:2494-502 pubmed
- Buhler M, Haas W, Gygi S, Moazed D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell. 2007;129:707-21 pubmed..Our findings indicate that polyadenylation by a TRAMP-like complex contributes to robust silencing of heterochromatic genes in fission yeast via the recruitment of the exosome and/or the RNAi machinery. ..
- Vagner S, Vagner C, Mattaj I. The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3'-end processing and splicing. Genes Dev. 2000;14:403-13 pubmed..The carboxy-terminal domain of PAP makes a direct and specific interaction with residues 17-47 of U2AF 65, implicating this interaction in the coupling of splicing and 3'-end formation. ..
- Martin G, Keller W. Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases. RNA. 2004;10:899-906 pubmed
- Hou Y. Unusual synthesis by the Escherichia coli CCA-adding enzyme. RNA. 2000;6:1031-43 pubmed
- 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
- Binns N, Masters M. Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU. Mol Microbiol. 2002;44:1287-98 pubmed..We show that InfC discrimination reduces PcnB production fivefold. This is the first instance of this mechanism being used to limit severely the production of a potentially toxic product. ..
- Jasiecki J, Wegrzyn G. Growth-rate dependent RNA polyadenylation in Escherichia coli. EMBO Rep. 2003;4:172-7 pubmed..This may allow regulation of the stability of certain transcripts (those subjected to PAP I-dependent polyadenylation) in response to various growth conditions. ..
- Cao G, Sarkar N. Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci U S A. 1992;89:10380-4 pubmed..The identification of a gene encoding bacterial poly(A) polymerase opens the way for the study of the biosynthesis and function of bacterial polyadenylylated mRNA. ..
- Mellman D, Gonzales M, Song C, Barlow C, Wang P, Kendziorski C, et al. A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs. Nature. 2008;451:1013-7 pubmed publisher..The results reveal a mechanism for the integration of nuclear phosphoinositide signals and a method for regulating gene expression. ..
- Keller C, Woolcock K, Hess D, Buhler M. Proteomic and functional analysis of the noncanonical poly(A) polymerase Cid14. RNA. 2010;16:1124-9 pubmed publisher..In contrast, no physical link to chromatin has been identified, although gene expression profiling revealed that efficient silencing of a few heterochromatic genes depends on Cid14 and/or Air1. ..
- Sillero M, de Diego A, Silles E, Osorio H, Sillero A. Polyphosphates strongly inhibit the tRNA dependent synthesis of poly(A) catalyzed by poly(A) polymerase from Saccharomyces cerevisiae. FEBS Lett. 2003;550:41-5 pubmed..3 microM) changed the Hill coefficient (n(H)) from 1 (control) to about 1.3 and 1.6, respectively. In (b), the inhibition by P(4) and P(15) decreased V and modified only slightly the K(m) values of the enzyme towards tRNA. ..
- Marujo P, Hajnsdorf E, Le Derout J, Andrade R, Arraiano C, Regnier P. RNase II removes the oligo(A) tails that destabilize the rpsO mRNA of Escherichia coli. RNA. 2000;6:1185-93 pubmed..These in vivo data demonstrate that RNase II protects mRNAs ending by stable terminal hairpins, such as primary transcripts, from degradation by poly(A)-dependent ribonucleases. ..
- Houseley J, Tollervey D. Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep. 2006;7:205-11 pubmed..Trf5p co-purified with Mtr4p and Air1p, indicating that it forms a complex, designated TRAMP5, that has functions that partially overlap with the TRAMP complex. ..
- Hajnsdorf E, Regnier P. E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA. J Mol Biol. 1999;286:1033-43 pubmed..We conclude that 5' extremities modulate the poly(A)-dependent degradation of mRNA fragments and that the 5' cleavage by RNase E at M3 activates the chemical degradation of the rpsO mRNA. ..
- Chen L, Sheppard T. Chain termination and inhibition of Saccharomyces cerevisiae poly(A) polymerase by C-8-modified ATP analogs. J Biol Chem. 2004;279:40405-11 pubmed..Base-modified ATP analogs may exert their biological effects through polyadenylation inhibition and thus may provide useful tools for investigating polyadenylation biochemistry within cells. ..
- Kuai L, Fang F, Butler J, Sherman F. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2004;101:8581-6 pubmed..For at least one rRNA type, the polyadenylation preferentially occurs on the precursor rather than the mature product. The existence of polyadenylated rRNAs may reflect a quality-control mechanism of rRNA biogenesis. ..
- Szalewska Pałasz A, Wrobel B, Wegrzyn G. Rapid degradation of polyadenylated oop RNA. FEBS Lett. 1998;432:70-2 pubmed..Analysis of oop RNA and its degradation product isolated from Escherichia coli cells suggests that both polyadenylated and non-modified oop transcripts can act as antisense RNA. ..
- Nakanishi T, Kubota H, Ishibashi N, Kumagai S, Watanabe H, Yamashita M, et al. Possible role of mouse poly(A) polymerase mGLD-2 during oocyte maturation. Dev Biol. 2006;289:115-26 pubmed..These results suggest that mGLD-2 may act in the ooplasm on the progression of metaphase I to metaphase II during oocyte maturation. ..
- Rouhana L, Wang L, Buter N, Kwak J, Schiltz C, Gonzalez T, et al. Vertebrate GLD2 poly(A) polymerases in the germline and the brain. RNA. 2005;11:1117-30 pubmed..We suggest that mammalian GLD2 poly(A) polymerases are important in synaptic translation, and in polyadenylation throughout the soma. ..
- Kwak J, Wang L, Ballantyne S, Kimble J, Wickens M. Mammalian GLD-2 homologs are poly(A) polymerases. Proc Natl Acad Sci U S A. 2004;101:4407-12 pubmed..We use the same tethered assay to identify human and mouse poly(A) polymerases related to GLD-2. This may provide entrees to previously uncharacterized modes of polyadenylation in mammalian cells. ..
- 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. ..
- Betat H, Rammelt C, Martin G, Mörl M. Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities. Mol Cell. 2004;15:389-98 pubmed..This seems to be the prerequisite for the observed reprogramming of the catalytic center of PAP to incorporate a sequence of defined length and composition instead of long stretches of A residues. ..
- Wang S, Stevenson A, Kearsey S, Watt S, Bahler J. Global role for polyadenylation-assisted nuclear RNA degradation in posttranscriptional gene silencing. Mol Cell Biol. 2008;28:656-65 pubmed
- Sohlberg B, Huang J, Cohen S. The Streptomyces coelicolor polynucleotide phosphorylase homologue, and not the putative poly(A) polymerase, can polyadenylate RNA. J Bacteriol. 2003;185:7273-8 pubmed..In contrast, a Streptomyces coelicolor polynucleotide phosphorylase homologue that exhibits polyadenylation activity may account for the poly(A) tails found in this organism. ..
- Yue D, Maizels N, Weiner A. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996;2:895-908 pubmed..One implication of these data is that there may have been intraconversion of CCA-adding and poly(A) polymerase activities early in evolution...
- Mohanty B, Kushner S. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol Microbiol. 1999;34:1094-108 pubmed..6% of their poly(A) tails. Cloning and sequencing of cDNAs derived from lpp, 23S and 16S rRNA revealed that, during exponential growth, C and U residues were polymerized into poly(A) tails in a transcript-dependent manner. ..
- Stevenson A, Norbury C. The Cid1 family of non-canonical poly(A) polymerases. Yeast. 2006;23:991-1000 pubmed..Cid1-like proteins have important roles in diverse biological processes, including RNA surveillance pathways, DNA integrity checkpoint responses and RNAi-dependent heterochromatin formation. ..
- Raynal L, Krisch H, Carpousis A. The Bacillus subtilis nucleotidyltransferase is a tRNA CCA-adding enzyme. J Bacteriol. 1998;180:6276-82 pubmed..subtilis has a PAP similar to E. coli PAP I. Thus, the activity involved in RNA 3' polyadenylation in the gram-positive bacteria apparently resides in an enzyme distinct from its counterpart in gram-negative bacteria. ..