Genomes and Genes
Summary: A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
- Sawicki D, Wang T, Sawicki S. The RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virus. J Gen Virol. 2001;82:385-96 pubmed..Failure originally to find TIs and TF cores was probably due to overdigestion with RNase A. ..
- Paul A, van Boom J, Filippov D, Wimmer E. Protein-primed RNA synthesis by purified poliovirus RNA polymerase. Nature. 1998;393:280-4 pubmed..Uridylylated VPg can then prime the transcription of polyadenylate RNA by 3Dpol to produce VPg-linked poly(U). Initiation of transcription of the poliovirus genome from the polyadenylated 3' end therefore depends on VPg. ..
- Jelenc P, Kurland C. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc Natl Acad Sci U S A. 1979;76:3174-8 pubmed
- Ichinohe T, Tamura S, Kawaguchi A, Ninomiya A, Imai M, Itamura S, et al. Cross-protection against H5N1 influenza virus infection is afforded by intranasal inoculation with seasonal trivalent inactivated influenza vaccine. J Infect Dis. 2007;196:1313-20 pubmed
- Rissland O, Norbury C. The Cid1 poly(U) polymerase. Biochim Biophys Acta. 2008;1779:286-94 pubmed publisher..Here, we review the literature on Cid1, other PUPs and uridylation, a conserved and previously under-appreciated mechanism of RNA regulation. ..
- You S, Rice C. 3' RNA elements in hepatitis C virus replication: kissing partners and long poly(U). J Virol. 2008;82:184-95 pubmed..This suggests that the poly(U/UC) tract does not function simply as an unstructured spacer to position the kissing-loop elements. ..
- Janouskovec J, Horak A, Obornik M, Lukes J, Keeling P. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Natl Acad Sci U S A. 2010;107:10949-54 pubmed publisher..g., ciliates, Cryptosporidium, and Phytophthora)...
- Coltri P, Guimar es B, Granato D, Luz J, Teixeira E, Oliveira C, et al. Structural insights into the interaction of the Nip7 PUA domain with polyuridine RNA. Biochemistry. 2007;46:14177-87 pubmed publisher..This work provides experimental verification that the PUA domain mediates Nip7 interaction with RNA and reveals that the preference for interaction with polyuridine sequences is conserved in Archaea and eukaryotic Nip7 proteins...
- Yi M, Lemon S. 3' nontranslated RNA signals required for replication of hepatitis C virus RNA. J Virol. 2003;77:3557-68 pubmed
- Fischer S, Benz J, Späth B, Maier L, Straub J, Granzow M, et al. The archaeal Lsm protein binds to small RNAs. J Biol Chem. 2010;285:34429-38 pubmed publisher..The deletion of the lsm gene is viable, resulting in a pleiotropic phenotype, indicating that the haloarchaeal Lsm is involved in many cellular processes, which is in congruence with the number of protein interaction partners...
- Scholdberg T, Nechev L, Merritt W, Harris T, Harris C, Lloyd R, et al. Mispairing of a site specific major groove (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA Adduct of butadiene diol epoxide with deoxyguanosine: formation of a dA(anti).dG(anti) pairing interaction. Chem Res Toxicol. 2005;18:145-53 pubmed..R., Nechev, L. N., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2000) Env. Mol. Mutagen. 35, 48-56]. ..
- Kankia B. Mg2+-induced triplex formation of an equimolar mixture of poly(rA) and poly(rU). Nucleic Acids Res. 2003;31:5101-7 pubmed..The phase boundary corresponding to the transition between double and triple helical conformations lies near physiological salt concentrations and temperature. ..
- Olsen A, Morrey J, Smee D, Sidwell R. Correlation between breakdown of the blood-brain barrier and disease outcome of viral encephalitis in mice. Antiviral Res. 2007;75:104-12 pubmed..In general, it was found that evaluation of BBB permeability was a more sensitive indicator of disease outcome and the antiviral efficacy Ampligen than either weight change or brain viral titers...
- Xu Y, Wang B, Zhu Y. Identification of proteins expressed at extremely low level in Arabidopsis leaves. Biochem Biophys Res Commun. 2007;358:808-12 pubmed..Our results suggest that polyU or similar media may be combined with 2-DE techniques to identify cellular proteins with extremely low transcription levels to fulfill specific research needs. ..
- Iwama M, Ogawa Y, Ohgi K, Tsuji T, Irie M. Enzymatic properties of sialic acid binding lectin from Rana catesbeiana modified with a water-soluble carbodiimide in the presence of various nucleophiles. Biol Pharm Bull. 2001;24:1366-9 pubmed..physiologic ionic strength conditions; (ii) RNase activity of the modified cSBL towards single stranded RNA and poly U decreased, while the activity towards poly C was unaffected; (iii) the base preference of the B2 base recognition ..
- Volker J, Klump H, Manning G, Breslauer K. Counterion association with native and denatured nucleic acids: an experimental approach. J Mol Biol. 2001;310:1011-25 pubmed..We discuss some of the broader implications of these measurements/results in terms of nucleic acid melting in multicomponent systems, in terms of probing counterion environments, and in terms of potential regulatory mechanisms. ..
- Zhu H, Zhou H, Hasman R, Lou H. Hu proteins regulate polyadenylation by blocking sites containing U-rich sequences. J Biol Chem. 2007;282:2203-10 pubmed..These studies identify a novel group of mammalian polyadenylation regulators. Furthermore, they define a previously unknown nuclear function of Hu proteins. ..
- Snoussi K, Bulte J, Guéron M, van Zijl P. Sensitive CEST agents based on nucleic acid imino proton exchange: detection of poly(rU) and of a dendrimer-poly(rU) model for nucleic acid delivery and pharmacology. Magn Reson Med. 2003;49:998-1005 pubmed
- de Juan A, Izquierdo Ridorsa A, Tauler R, Fonrodona G, Casassas E. A soft-modeling approach to interpret thermodynamic and conformational transitions of polynucleotides. Biophys J. 1997;73:2937-48 pubmed
- Ponamarev M, She Y, Zhang L, Robinson B. Proteomics of bovine mitochondrial RNA-binding proteins: HES1/KNP-I is a new mitochondrial resident protein. J Proteome Res. 2005;4:43-52 pubmed..3 and may be involved in several disorders mapped to that region. Thus, HES1/KNP-I is a proven mitochondrial resident protein with apparent tight membrane association and tentative RNA-binding properties. ..
- Patterson M, Poussard A, Taylor K, Seregin A, Smith J, Peng B, et al. Rapid, non-invasive imaging of alphaviral brain infection: reducing animal numbers and morbidity to identify efficacy of potential vaccines and antivirals. Vaccine. 2011;29:9345-51 pubmed publisher..Based on our data from the imaging model, we confirmed the usefulness of this technology in preclinical research by demonstrating the efficacy of Ampligen, a TLR-3 agonist, in preventing CNS invasion. ..
- Oshima T. Unique polyamines produced by an extreme thermophile, Thermus thermophilus. Amino Acids. 2007;33:367-72 pubmed..In this new pathway spermidine is not synthesized from putrescine. Reverse genetic studies indicated that the unique polyamines are synthesized from spermidine. ..
- Zuber H, Scheer H, Ferrier E, Sement F, Mercier P, Stupfler B, et al. Uridylation and PABP Cooperate to Repair mRNA Deadenylated Ends in Arabidopsis. Cell Rep. 2016;14:2707-17 pubmed publisher..Taken together, our results uncover a role for uridylation and PABP in repairing mRNA deadenylated ends and reveal that uridylation plays diverse roles in eukaryotic mRNA metabolism. ..
- Armstrong J, McMahon D, Huang X, Pazin G, Gupta P, Rinaldo C, et al. A phase I study of ampligen in human immunodeficiency virus-infected subjects. J Infect Dis. 1992;166:717-22 pubmed..This effect of ampligen and the fact that it has been shown to act synergistically with zidovudine against HIV in vitro suggest that the combination might be tried clinically in patients. ..
- Sorokin V, Valeev V, Gladchenko G, Degtiar M, Karachevtsev V, Blagoi Y. Mg2+ ion effect on conformational equilibrium of poly A . 2 poly U and poly A poly U in aqueous solutions. Int J Biol Macromol. 2003;31:223-33 pubmed..2 poly U (A2U) and poly A . poly U (AU) solutions at low (0.01 M Na(+)) and high (0.1 M Na(+)) ionic strengths...
- Leimoni I, Sideris D, Fragoulis E. Purification from normal human plasma and biochemical characterization of a ribonuclease specific for poly(C) and poly(U). Arch Biochem Biophys. 2003;413:83-90 pubmed..5. Comparison between other known plasma RNases and the human plasma ribonuclease described here indicated a variety of differences in their biochemical and catalytic properties. ..
- Ericson G, Minchew P, Wollenzien P. Structural changes in base-paired region 28 in 16 S rRNA close to the decoding region of the 30 S ribosomal subunit are correlated to changes in tRNA binding. J Mol Biol. 1995;250:407-19 pubmed..Models that include a hydrogen bond interaction between A1394 and G1392 account for the G926 reactivity in the wild-type sequence and account for the effects of most of the mutations in changing the G926 reactivity. ..
- Gilbert C, Barabé F, Rollet Labelle E, Bourgoin S, McColl S, Damaj B, et al. Evidence for a role for SAM68 in the responses of human neutrophils to ligation of CD32 and to monosodium urate crystals. J Immunol. 2001;166:4664-71 pubmed
- Borowski C, Rodnina M, Wintermeyer W. Truncated elongation factor G lacking the G domain promotes translocation of the 3' end but not of the anticodon domain of peptidyl-tRNA. Proc Natl Acad Sci U S A. 1996;93:4202-6 pubmed..The G domain's intramolecular interactions are likely to be modulated by GTP binding and hydrolysis. ..
- Kelley R, Wang J, Bell L, Kuroda M. Sex lethal controls dosage compensation in Drosophila by a non-splicing mechanism. Nature. 1997;387:195-9 pubmed..Thus, this well characterized alternative splicing factor regulates at least one target transcript by a distinct mechanism. ..
- Hosaka T, Tamehiro N, Chumpolkulwong N, Hori Takemoto C, Shirouzu M, Yokoyama S, et al. The novel mutation K87E in ribosomal protein S12 enhances protein synthesis activity during the late growth phase in Escherichia coli. Mol Genet Genomics. 2004;271:317-24 pubmed..We propose that the aberrant activation of protein synthesis at the late growth phase is caused by the increased stability of the ribosome. ..
- Westwood A, Elvin S, Healey G, Williamson E, Eyles J. Immunological responses after immunisation of mice with microparticles containing antigen and single stranded RNA (polyuridylic acid). Vaccine. 2006;24:1736-43 pubmed..05). These data demonstrate, for the first time, that appropriately formulated ssRNA can act as a potent adjuvant and modulator of adaptive immunological responses. ..
- Králíková S, Budesinsky M, Barvik I, Masojidkova M, Tocík Z, Rosenberg I. Synthesis and properties of ApA analogues with shortened phosphonate internucleotide linkage. Nucleosides Nucleotides Nucleic Acids. 2011;30:524-43 pubmed publisher..Potential usefulness of the ?-hydroxy-phosphonate linkage in modified oligoribonucleotides is discussed. ..
- Sinet M, Pocidalo J. [Are immunomodulators capable to improve the activity of nucleoside antiretroviral agents?]. Pathol Biol (Paris). 1993;41:794-8 pubmed..virus infection, the antiretroviral effect of zidovudine is enhanced by combination with poly I poly C or poly A poly U. Polyribonucleotides also enhance the inhibitory effect of zidovudine on HIV replication in lymphocyte T or ..
- Hirokawa G, Kiel M, Muto A, Kawai G, Igarashi K, Kaji H, et al. Binding of ribosome recycling factor to ribosomes, comparison with tRNA. J Biol Chem. 2002;277:35847-52 pubmed publisher..The binding of RRF and tRNA to ribosomes was influenced by Mg(2+) and NH(4)(+) ions in a similar manner...
- Hanawa Suetsugu K, Takagi M, Inokuchi H, Himeno H, Muto A. SmpB functions in various steps of trans-translation. Nucleic Acids Res. 2002;30:1620-9 pubmed
- Yagodina L. Interaction of the bacterial ribonuclease binase with the polypeptide inhibitor barstar based on kinetic data on poly(U) hydrolysis. Biochemistry (Mosc). 2001;66:319-22 pubmed..Both ethanol and NaCl enhance the inhibition by barstar. This suggests that the binding of barstar with binase is probably due to the interaction of hydrophobic sites rather than by electrostatic interaction between amino acid residues. ..
- Nameki N, Tadaki T, Muto A, Himeno H. Amino acid acceptor identity switch of Escherichia coli tmRNA from alanine to histidine in vitro. J Mol Biol. 1999;289:1-7 pubmed..These results indicate that the first alanine residue of the tag-peptide is actually derived from that aminoacylated to tmRNA and is substitutable by other amino acids during the trans -translation processes. ..
- Abrahams J, Acampo J, Kraal B, Bosch L. The influence of tRNA located at the P-site on the turnover of EF-Tu.GTP on ribosomes. Biochimie. 1991;73:1089-92 pubmed..GTP than ribosomes with an empty P-site. The data suggest that this is mainly caused by an increased affinity of EF-Tu.GTP for ribosomes with a filled P-site rather than by an enhanced reactivity of the GTPase centre. ..
- Romero F, Ramos Morales F, Dominguez A, Rios R, Schweighoffer F, Tocque B, et al. Grb2 and its apoptotic isoform Grb3-3 associate with heterogeneous nuclear ribonucleoprotein C, and these interactions are modulated by poly(U) RNA. J Biol Chem. 1998;273:7776-81 pubmed..These findings suggest that the Grb2/Grb3-3-hnRNP C interactions might fulfill different biological functions. ..
- Bricker B. Differentiation of hard-to-type bacterial strains by RNA mismatch cleavage. Biotechniques. 1999;27:321-4, 326 pubmed..Of the remaining seven biovars (all of which are Brucella abortus strains), three subgroups were identified. The method should be applicable to all hard-to-subtype bacterial strains. ..
- Landwehr M, Curth U, Urbanke C. A dimeric mutant of the homotetrameric single-stranded DNA binding protein from Escherichia coli. Biol Chem. 2002;383:1325-33 pubmed..In conclusion, nucleic acid binding to homotetrameric SSB must take place across both dimers to achieve functionally correct binding. ..
- Osawa K, Urata H, Sawai H. Chiral selection in oligoadenylate formation in the presence of a metal ion catalyst or poly(U) template. Orig Life Evol Biosph. 2005;35:213-23 pubmed..In contrast, L-ImpA or racemic DL-ImpA polymerized far less efficiently on the poly(U) template, demonstrating that chiral selection takes place in the poly(U) template-directed oligoadenylate formation. ..
- Okamoto Hosoya Y, Hosaka T, Ochi K. An aberrant protein synthesis activity is linked with antibiotic overproduction in rpsL mutants of Streptomyces coelicolor A3(2). Microbiology. 2003;149:3299-309 pubmed..The authors propose that the aberrant activation of protein synthesis caused by the increased stability of the ribosome is responsible for the remarkable enhancement of antibiotic production in the K88E and P91S mutants. ..
- del Toro Duany Y, Jungblut S, Schmidt A, Klostermeier D. The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain. Nucleic Acids Res. 2008;36:5882-95 pubmed publisher..This inhibitory effect of the topoisomerase domain decelerates the progression of reverse gyrase through the nucleotide cycle, possibly providing optimal coordination of ATP hydrolysis with the complex reaction of DNA supercoiling...
- Luo G. Cellular proteins bind to the poly(U) tract of the 3' untranslated region of hepatitis C virus RNA genome. Virology. 1999;256:105-18 pubmed..Interaction of these cellular proteins with the HCV 3' UTR is probably involved in regulation of translation and/or replication of the HCV RNA genome. ..
- Dresios J, Derkatch I, Liebman S, Synetos D. Yeast ribosomal protein L24 affects the kinetics of protein synthesis and ribosomal protein L39 improves translational accuracy, while mutants lacking both remain viable. Biochemistry. 2000;39:7236-44 pubmed..Protein L39 is the first protein of the 60S ribosomal subunit implicated in translational accuracy. ..
- van Ooij M, Polacek C, Glaudemans D, Kuijpers J, van Kuppeveld F, Andino R, et al. Polyadenylation of genomic RNA and initiation of antigenomic RNA in a positive-strand RNA virus are controlled by the same cis-element. Nucleic Acids Res. 2006;34:2953-65 pubmed..The possibility of RNA replication independent of oriR and poly(A) demonstrate that highly debilitated viruses are able to survive by utilizing 'emergence', perhaps atavistic, mechanisms. ..
- Bergamini A, Ercoli L, Perno C. [Inhibition of alfa interferon and ampligen of human immunodeficiency virus (HIV) replication in monocyte-macrophage subpopulations]. Medicina (Firenze). 1990;10:34-6 pubmed..Finally, HIV replication in chronically-infected M/M was not affected by alpha-IFN. These results suggest that alpha-IFN might be useful in combination with other anti-HIV drugs in the therapy of HIV-related disease. ..
- Kell A, Stoddard M, Li H, Marcotrigiano J, Shaw G, Gale M. Pathogen-Associated Molecular Pattern Recognition of Hepatitis C Virus Transmitted/Founder Variants by RIG-I Is Dependent on U-Core Length. J Virol. 2015;89:11056-68 pubmed publisher..Thus, recognition of T/F variants by RIG-I could significantly impact the transition from acute to chronic infection. ..