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.
Publications181 found, 100 shown here
- Structural insights into the interaction of the Nip7 PUA domain with polyuridine RNAPatricia P Coltri
Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, LNLS, Rua Giuseppe Maximo Scolfaro 10000, P O Box 6192, CEP13083 970, Campinas SP, Brazil
Biochemistry 46:14177-87. 2007..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...
- Ampligen: a potential toll-like 3 receptor adjuvant for immunotherapy of cancerB Jasani
Departments of Pathology, School of Medicine, Cardiff University, Cardiff, Wales, UK
Vaccine 27:3401-4. 2009....
- Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functionsMaria A Xaplanteri
Laboratory of Biochemistry, School of Medicine, University of Patras GR-26500 Patras, Greece
Nucleic Acids Res 33:2792-805. 2005..However, they exhibited higher reactivity toward puromycin and enhanced tRNA-translocation efficiency. These results suggest an essential role for polyamines in the structural and functional integrity of the large ribosomal subunit...
- TLR3 is essential for the induction of protective immunity against Punta Toro Virus infection by the double-stranded RNA (dsRNA), poly(I:C12U), but not Poly(I:C): differential recognition of synthetic dsRNA moleculesBrian B Gowen
Institute for Antiviral Research, Utah State University, Logan, Utah 84341, USA
J Immunol 178:5200-8. 2007..We conclude that TLR3 is essential to the induction of antiviral activity elicited by poly(I:C(12)U), which does not appear to be recognized by the cytosolic sensor of poly(I:C), melanoma differentiation-associated gene-5...
- Intranasal immunization with H5N1 vaccine plus Poly I:Poly C12U, a Toll-like receptor agonist, protects mice against homologous and heterologous virus challengeTakeshi Ichinohe
Department of Pathology, National Institute of Infectious Diseases, 4 7 1 Gakuen, Musashimurayama shi, Tokyo 208 0011, Japan
Microbes Infect 9:1333-40. 2007....
- Cross-protection against H5N1 influenza virus infection is afforded by intranasal inoculation with seasonal trivalent inactivated influenza vaccineTakeshi Ichinohe
Department of Pathology, National Institute of Infectious Diseases, Musashimurayama shi, Tokyo, Japan
J Infect Dis 196:1313-20. 2007..We evaluated the ability of currently licensed seasonal influenza vaccine to confer cross-protection against highly pathogenic H5N1 influenza virus in mice...
- Protein-primed RNA synthesis by purified poliovirus RNA polymeraseA V Paul
Department of Molecular Genetics and Microbiology, School of Medicine, Health Science Center, State University of New York, Stony Brook 11794 5222, USA
Nature 393:280-4. 1998..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...
- The Cid1 poly(U) polymeraseOlivia S Rissland
Sir William Dunn School of Pathology, University of Oxford, UK
Biochim Biophys Acta 1779:286-94. 2008..Here, we review the literature on Cid1, other PUPs and uridylation, a conserved and previously under-appreciated mechanism of RNA regulation...
- Uridine addition after microRNA-directed cleavageBinzhang Shen
Department of Genetics, Harvard Medical School, and Department of Molecular Biology, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
Science 306:997. 2004..This 3' uridine addition, as shown for Arabidopsis, is correlated with decapping and 5' shortening of the cleaved products, suggesting a mechanistic step in the miRNA-directed mRNA decay mechanism...
- The RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virusD Sawicki
Department of Microbiology and Immunology, Medical College of Ohio, 3055 Arlington Avenue, Toledo, OH 43614, USA
J Gen Virol 82:385-96. 2001..Failure originally to find TIs and TF cores was probably due to overdigestion with RNase A...
- Probing the substrate specificity of Escherichia coli RNase E using a novel oligonucleotide-based assayVladimir R Kaberdin
Max F Perutz Laboratories, Department of Microbiology and Genetics, University Department at the Vienna Biocenter, Dr Bohrgasse 9 4, A 1030 Vienna, Austria
Nucleic Acids Res 31:4710-6. 2003..Moreover, the simplicity and efficiency of the proposed assay suggest that it can be a valuable tool not only for the characterization of RNase E homologs but also for the analysis of other site-specific nucleases...
- Characterization of mammalian eIF2A and identification of the yeast homologWendy L Zoll
Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106 4935, USA
J Biol Chem 277:37079-87. 2002..The lack of any apparent phenotype in the DeltaeIF2A strain suggests that eIF2A functions in a minor pathway, perhaps internal initiation or in the translation of a small number of specific mRNAs...
- Binding of ribosome recycling factor to ribosomes, comparison with tRNAGo Hirokawa
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
J Biol Chem 277:35847-52. 2002..The binding of RRF and tRNA to ribosomes was influenced by Mg(2+) and NH(4)(+) ions in a similar manner...
- Mg2+ ion effect on conformational equilibrium of poly A . 2 poly U and poly A poly U in aqueous solutionsVictor A Sorokin
Department of Molecular Biophysics, Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 61103, Ukraine
Int J Biol Macromol 31:223-33. 2003..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...
- RNA recognition motif-type RNA-binding proteins in Trypanosoma cruzi form a family involved in the interaction with specific transcripts in vivoJavier G De Gaudenzi
Instituto de Investigaciones Biotecnológicas Instituto Tecnológico de Chascomús, CONICET UNSAM, 1650 San Martin, Provincia de Buenos Aires, Argentina
J Biol Chem 278:18884-94. 2003..Altogether, these results suggest that TcRBPs might be modulated in vivo, to favor or preclude the interaction with specific transcripts in a developmentally regulated manner...
- Polyadenylation regulates the stability of Trypanosoma brucei mitochondrial RNAsChristopher M Ryan
Department of Microbiology and the Witebsky Center for Microbial Pathogenesis and Immunology, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214, USA
J Biol Chem 278:32753-62. 2003..These experiments demonstrate that the poly(A) tail can act as a cis-acting element to facilitate degradation of T. brucei mitochondrial mRNAs...
- Various effects of paromomycin on tmRNA-directed trans-translationToshiharu Takahashi
Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Hirosaki University, Hirosaki 036 8561 Japan
J Biol Chem 278:27672-80. 2003..The effect of paromomycin on trans-translation differs substantially from that on canonical translation, in which it induces miscoding by modulating the A site of the decoding helix of the small subunit RNA of the ribosome...
- Formation of 70S ribosomes: large activation energy is required for the adaptation of exclusively the small ribosomal subunitGregor Blaha
, Berlin, Germany
Biophys Chem 96:153-61. 2002....
- Species-specific and isoform-specific RNA binding of human and mouse fragile X mental retardation proteinsRobert B Denman
Laboratory of Molecular Neurobiology, Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
Biochem Biophys Res Commun 292:1063-9. 2002..Finally, these data demonstrate that each FMRP variant binds RNAs uniquely, resulting in a set of proteins with differing affinities...
- Poly(A)- and poly(U)-specific RNA 3' tail shortening by E. coli ribonuclease EH Huang
Department of Genetics, Stanford University School of Medicine, California 94305 5120, USA
Nature 391:99-102. 1998..The ability of RNase E to shorten poly(A) tails, together with the effect of tail length on endonucleolytic cleavage within primary transcripts, suggests a mechanism by which RNase E may exercise overall control over RNA decay...
- Functional implications of ribosomal protein L2 in protein biosynthesis as shown by in vivo replacement studiesM Uhlein
Max Delbruck Centrum fur Molekulare Medizin, Robert Rossle Str 10, D 13125 Berlin, Federal Republic of Germany
Biochem J 331:423-30. 1998..Replacement of this histidine residue in the human and archaebacterial proteins by glycine, arginine or alanine had no effect on ribosome assembly, but strongly reduced the translational activity of ribosomes containing these mutants...
- Preferential degradation of polyadenylated and polyuridinylated RNAs by the bacterial exoribonuclease polynucleotide phosphorylaseI Lisitsky
Department of Biology, Israel Institute of Technology, Haifa, Israel
Eur J Biochem 261:468-74. 1999..The high affinity of PNPase for polyadenylated RNA molecules may be part of the molecular mechanism by which polyadenylated RNA is preferentially degraded in bacterial cells...
- Kinetic and product distribution analysis of human eosinophil cationic protein indicates a subsite arrangement that favors exonuclease-type activityE Boix
Departament de Bioquimica i Biologia Molecular, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
J Biol Chem 274:15605-14. 1999..The differences in the multisubsites structure could explain the reduced catalytic efficiency of ECP and the shift from an endonuclease to an exonuclease-type mechanism...
- Mutagenesis of glutamine 290 in Escherichia coli and mitochondrial elongation factor Tu affects interactions with mitochondrial aminoacyl-tRNAs and GTPase activitySenyene Eyo Hunter
Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, North Carolina 27599 3290, USA
Biochemistry 43:6917-27. 2004..Surprisingly, while E. coli EF-Tu Q290L is more active in polymerization with mitochondrial Phe-tRNA(Phe), this variant has low activity in the formation of a stable ternary complex with mitochondrial aa-tRNA...
- Identification of an RNA binding specificity for the potential splicing factor TLSA Lerga
Inserm U528, Institut Curie-Recherche, 26 rue d'Ulm, 75248 Paris, Cedex 05, France
J Biol Chem 276:6807-16. 2001..Hence, our results help define the role of the specific interaction of TLS with RNA during the splicing process of a pre-mRNA...
- Poly(rC) binding proteins mediate poliovirus mRNA stabilityK E Murray
Department of Microbiology, University of Colorado Health Sciences Center, Denver 80262, USA
RNA 7:1126-41. 2001....
- Counterion association with native and denatured nucleic acids: an experimental approachJ Volker
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway 08854, USA
J Mol Biol 310:1011-25. 2001..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...
- Poly(rA).poly(rU) with Ni(2+) ions at different temperatures: infrared absorption and vibrational circular dichroism spectroscopyV Andrushchenko
Department of Chemistry, Faculty of Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
J Biomol Struct Dyn 19:889-906. 2002..VCD spectroscopy demonstrated significant advantages over infrared absorption or the related electronic CD spectroscopy...
- Protein synthesis by single ribosomesFrancesco Vanzi
Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6083, USA
RNA 9:1174-9. 2003..This work opens the way for application of biophysical techniques, originally developed for the classical motor proteins, to the understanding of protein biosynthesis...
- Conformational change in the 16S rRNA in the Escherichia coli 70S ribosome induced by P/P- and P/E-site tRNAPhe bindingJames W Noah
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA
Biochemistry 42:14386-96. 2003....
- A ribonuclease from Chinese ginseng (Panax ginseng) flowersH X Wang
Department of Microbiology, China Agricultural University, Beijing and Key Laboratory of Agro-microbial Resource and Application, Ministry of Agriculture, Beijing, China
Protein Expr Purif 33:195-9. 2004..The characteristics of this ribonuclease were different from those of ribonuclease previously purified from ginseng roots...
- Intercalation of ethidium into triple-strand poly(rA).2poly(rU): a thermodynamic and kinetic studyB Garcia
, Universidad de Burgos, , 09001 Burgos, Spain
J Phys Chem B 110:16131-8. 2006....
- [Mutation analysis of functional role of amino acid residues in domain IV of elongation factor G]A A Kovtun
Mol Biol (Mosk) 40:850-6. 2006..These loops are located at the tip of domain IV and close to the decoding center of the 30S ribosomal subunit upon EF-G interaction with the ribosome. The functional role of EF-G and its domain IV in ribosomal translocation is discussed...
- The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factorRose Marie Jenvert
School of Life Sciences, Södertörns högskola, S 141 04 Huddinge, Sweden
J Mol Biol 365:764-72. 2007..This suggests that the N-terminal domain can activate stringent factor in trans. It is also shown that this activation is dependent on unacylated tRNA...
- Hu proteins regulate polyadenylation by blocking sites containing U-rich sequencesHui Zhu
Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
J Biol Chem 282:2203-10. 2007..These studies identify a novel group of mammalian polyadenylation regulators. Furthermore, they define a previously unknown nuclear function of Hu proteins...
- Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerasesHyundae D Cho
Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195 7350, USA
Proc Natl Acad Sci U S A 104:54-9. 2007..Collaboration between RNA and protein in the form of a ribonucleoprotein template may help to explain the evolutionary diversity of the nucleotidyltransferase family...
- Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachineEkaterini C Kouvela
Laboratory of Biochemistry, School of Medicine, University of Patras, GR 26500 Patras, Greece
Nucleic Acids Res 35:5108-19. 2007..Our results support the notion that 5S rRNA serves as a signal transducer between regions of 23S rRNA responsible for principal ribosomal functions...
- [The nature of different influence of Cd2+ ions on the conformation of three-stranded polyU-polyA-polyU and polyI-polyA-polyI in aqueous solution]V A Sorokin
Biofizika 52:1017-29. 2007..study the effect of Cd2+ ions on the conformational equilibrium of three-stranded (A21, A2U) and single-stranded (poly U, poly A and poly I) polynucleotides in aqueous solutions containing 0.1 M Na+ (pH 7)...
- New features of the ribosome and ribosomal inhibitors: non-enzymatic recycling, misreading and back-translocationWitold Szaflarski
Max Planck Institut fur Molekulare Genetik, AG Ribosomen, Ihnestr 73, D 14195 Berlin, Germany
J Mol Biol 380:193-205. 2008....
- Polyadenylation of genomic RNA and initiation of antigenomic RNA in a positive-strand RNA virus are controlled by the same cis-elementMark J M van Ooij
Department of Medical Microbiology, Nijmegen Center for Molecular Life Science, Radboud University, Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
Nucleic Acids Res 34:2953-65. 2006..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...
- Ice and the origin of lifeHauke Trinks
Technical University Hamburg-Harburg, D-21071 Hamburg, Germany
Orig Life Evol Biosph 35:429-45. 2005..Poly(A) was obtained in high yield and reached nucleotide chain lengths up to 400 containing predominantly 3'--> 5' linkages...
- Chiral selection in oligoadenylate formation in the presence of a metal ion catalyst or poly(U) templateKazuomi Osawa
Department of Applied Chemistry, Gunma University, Kiryu, Gunma, 376-8515, Japan
Orig Life Evol Biosph 35:213-23. 2005..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...
- The novel mutation K87E in ribosomal protein S12 enhances protein synthesis activity during the late growth phase in Escherichia coliT Hosaka
National Food Research Institute, 2 1 12 Kannondai, Tsukuba, Ibaraki 305 8642, Japan
Mol Genet Genomics 271:317-24. 2004..We propose that the aberrant activation of protein synthesis at the late growth phase is caused by the increased stability of the ribosome...
- Efficient and faithful in vitro translation of natural and synthetic mRNA with human ribosomesAna C Ferreras
, Facultad de Ciencias de la Salud, Maracay, Venezuela
Int J Mol Med 13:527-36. 2004..This efficient and faithful system is of interest for biochemical studies of the human translational machinery, as well as a basis for screening new drugs affecting protein synthesis in pathogenic microorganisms...
- Binding studies of cationic uridyl ribonucleic guanidine (RNG) to DNAMyunji Park
Department of Chemistry and Biochemistry, University of California at Santa Barbara, CA 93106, USA
Bioorg Med Chem Lett 15:3247-51. 2005..Results of the hybridization properties, sequence specificity, and the global conformation studies of the RNG U5.DNA A5 duplex are described...
- Proteomics of bovine mitochondrial RNA-binding proteins: HES1/KNP-I is a new mitochondrial resident proteinMikhail V Ponamarev
Department of Metabolism and Department of Structural Biology and Biochemistry, Hospital for Sick Children Research Institute, Toronto M5G 1X8, Ontario, Canada
J Proteome Res 4:43-52. 2005..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...
- Roles of the polypyrimidine tract and 3' noncoding region of hepatitis C virus RNA in the internal ribosome entry site-mediated translationH Wang
Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Institute of Medical Microbiology, Fudan University, Shanghai, PR China
Arch Virol 150:1085-99. 2005..The data above also indicated that the modulations of the IRES-mediated translation by the HCV 3'NCR and the polyU/UC tract were in a length-independent manner...
- Chromatographic investigation of macromolecular affinity interactionsGalina A Platonova
Institute of Macromolecular Compounds, Russian Academy of Sciences, St Petersburg 199004, Russia
J Chromatogr A 1065:75-81. 2005..Polyriboadenylic acid and poly(allylamine) were immobilized on macroporous disks (CIM disks). Quantitative parameters of affinity interactions between macromolecules were established using frontal analysis at different flow rates...
- The stabilizing contribution of thymine in duplexes of (dA)24 with (dU)24, (dT)24, (dU12-dT12), (dU-dT)12, (dU2-dT2)6, or (dU3-dT3)4: nearest neighbor and next-nearest neighbor effectsFrank B Howard
Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
Biopolymers 78:221-9. 2005..14 to 0.16, about the same or slightly less than values reported for polynucleotide duplexes and less than predicted from theoretical calculations...
- Mechanical studies of single ribosome/mRNA complexesFrancesco Vanzi
Pennsylvania Muscle Institute, Department of Bioengineering, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Biophys J 89:1909-19. 2005..The persistence length of poly(U) RNA homopolymer, modeled as a worm-like chain, was found to be 0.79 +/- 0.05 nm and the backbone elasticity was 900 +/- 140 pN, similar to values for single-stranded DNA...
- Fast in vitro translation system immobilized on a surface via specific biotinylation of the ribosomeRomualdas Stapulionis
Department of Physics and Astronomy, Aarhus University, Ny Munkegade, Bldg 1520, DK 8000 Arhus C, Denmark
Biol Chem 389:1239-49. 2008..Functional interactions of the immobilized ribosomes with various components of the protein synthesis apparatus are shown by use of surface plasmon resonance...
- Affinity labelling of rat liver ribosomal protein S26 by heptauridylate containing a 5'-terminal alkylating groupJ Stahl
Mol Biol Rep 9:219-22. 1984..The affinity labelling reaction could be abolished by (pU)14 and poly(U). From the results it is concluded that ribosomal protein S26 is located at the mRNA binding site of rat liver ribosomes...
- Characterization of RNA binding specificity of the Drosophila sex-lethal protein by in vitro ligand selectionE Sakashita
Department of Biology, Faculty of Science, Kobe University, Japan
Nucleic Acids Res 22:4082-6. 1994..These results suggest that Sxl recognizes and preferentially binds to a polyuridine stretch with a downstream AG sequence...
- Intrinsic molecular activities of the interferon-induced 2-5A-dependent RNaseB Dong
Department of Cancer Biology, Research Institute, Cleveland Clinic Foundation, Ohio 44195
J Biol Chem 269:14153-8. 1994..Reduced rates of 2-5A-dependent RNA cleavage were observed even after removal of ATP and chelation of divalent cations. However, optimal RNA cleavage rates required the presence of either manganese or magnesium and ATP...
- Sex lethal controls dosage compensation in Drosophila by a non-splicing mechanismR L Kelley
Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030, USA
Nature 387:195-9. 1997..Thus, this well characterized alternative splicing factor regulates at least one target transcript by a distinct mechanism...
- The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatographyG G Carmichael
J Biol Chem 250:3607-612. 1975....
- Role of the third strand in the binding of proflavine and pt-proflavine to poly(rA).2poly(rU): a thermodynamic and kinetic studyBegoña García
Departamento de Quimica, Universidad de Burgos, 09001 Burgos, Spain
J Phys Chem B 112:7132-9. 2008..Comparison with the binding of the same drugs to the duplex reveals that the occupation of the major groove in poly(rA).2poly(rU) by the third strand plays a critical role in the kinetic behavior...
- A family of cold-regulated RNA-binding protein genes in the cyanobacterium Anabaena variabilis M3N Sato
Laboratory of Life Science, Tokyo Gakugei University, Japan
Nucleic Acids Res 23:2161-7. 1995..Gel-filtration assay showed that all of the Rbp proteins have higher affinities to poly(G) and poly(U) than to poly(A) and poly(C)...
- Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficientsJ P Bond
Department of Chemistry, University of Wisconsin Madison 53706
Biophys J 67:825-36. 1994..With the best fitted values of ass and bss, our calculations of delta gamma PB are in close quantitative agreement with experimental observations on each of five nucleic acid order-disorder transitions...
- 3' Terminal oligo U-tract-mediated stimulation of decappingMan Gen Song
Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854 8082, USA
RNA 13:2356-65. 2007..These data suggest that following post-transcriptional oligo uridylation of an mRNA or mRNA fragment, the U-tract has the capacity to specifically stimulate 5' end decapping to expedite mRNA decay...
- Chemical shift perturbation studies of the interactions of the second RNA-binding domain of the Drosophila sex-lethal protein with the transformer pre-mRNA polyuridine tract and 3' splice-site sequencesS W Chi
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Taejon, Korea
Eur J Biochem 260:649-60. 1999..Taken together, the present results indicate that the interface residues that bind with GU8 and CUAGUG are much the same, but the role of the Y214 residue is clearly different between these two target sequences...
- Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesisNamthip Chumpolkulwong
RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan
Eur J Biochem 271:1127-34. 2004..Furthermore, when 14 mouse cDNA sequences were used as test templates, the protein yields of nine templates in the K42T system were 1.2-2 times higher than that of the wild-type...
- Effect of different mutations in ribosomal protein S5 of Escherichia coli on translational fidelityW Piepersberg
Mol Gen Genet 140:91-100. 1975..The part of the S5 polypeptide involved in control of translational fidelity is different from regions altered in spectinomycin resistant strains and in the alanyl-tRNA synthetase suppressor mutant...
- Effects of mutagenesis of Gln97 in the switch II region of Escherichia coli elongation factor Tu on its interaction with guanine nucleotides, elongation factor Ts, and aminoacyl-tRNATomas Navratil
Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, North Carolina 27599 3290, USA
Biochemistry 42:13587-95. 2003..Strikingly, the Q97P variant was completely inactive in ternary complex formation, accounting for its inability to function in polymerization. The structural basis of these observations is discussed...
- Peptide elongation factor 1 from yeasts: purification and biochemical characterization of peptide elongation factors 1 alpha and 1 beta (gamma) from Saccharomyces carlsbergensis and Schizosaccharomyces pombeM Miyazaki
Department of Molecular Biology, School of Science, Nagoya University, Aichi
J Biochem 103:508-21. 1988..pombe. Furthermore, a considerable amount of Phe-tRNA binding activity was distributed in the EF-1H (probably EF-1 alpha beta gamma) fraction from freshly prepared cell-free extracts of yeast...
- Phosphorylation of valyl-tRNA synthetase and elongation factor 1 in response to phorbol esters is associated with stimulation of both activitiesR C Venema
Department of Biochemistry, University of California, Riverside 92521
J Biol Chem 266:11993-8. 1991..These data suggest that stimulation of translational rates in response to PMA is mediated, at least in part, by phosphorylation of valyl-tRNA synthetase and EF-1...
- Phosphorylation of elongation factor 1 (EF-1) and valyl-tRNA synthetase by protein kinase C and stimulation of EF-1 activityR C Venema
Department of Biochemistry, University of California, Riverside 92521
J Biol Chem 266:12574-80. 1991..Thus, phosphorylation and activation of EF-1 by protein kinase C, which has been shown to occur in vitro as well as in reticulocytes, may have a role in PMA stimulation of translational rates...
- LRP130, a single-stranded DNA/RNA-binding protein, localizes at the outer nuclear and endoplasmic reticulum membrane, and interacts with mRNA in vivoNaoto Tsuchiya
Biochemistry Division, National Cancer Center Research Institute, 5 1 1 Tsukiji Chuo ku, Tokyo 104 0045, Japan
Biochem Biophys Res Commun 317:736-43. 2004..Taking all these results together, it is suggested that LRP130, a novel type of RNA-binding protein, associates with mRNA/mRNP complexes at the outside of NE and ER, and plays a role in control of mRNA metabolisms...
- Lack of correlation between interferon levels induced by polyribonucleotides and their antimetastatic effectM Sakurai
Department of Internal Medicine, National Cancer Center Hospital, Tokyo, Japan
Oncology 47:251-6. 1990..More extensive study of poly(A)poly(U) might give more fruitful results, which will give valuable information for future clinical trials of this lowly toxic promising agent...
- Heterogeneous nuclear ribonucleoprotein K contributes to angiotensin II stimulation of vascular endothelial growth factor mRNA translationDenis Feliers
Dept of Medicine Nephrology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, USA
Am J Physiol Renal Physiol 293:F607-15. 2007..This study shows that hnRNP K augments efficiency of VEGF mRNA translation stimulated by ANG II...
- Nicotinic stimulation modulates tyrosine hydroxylase mRNA half-life and protein binding to the 3'UTR in a manner that requires transcriptionDavid F Roe
Department of Neurobiology and Anatomy, The University of Texas Medical School, 5631 Fannin Street, Houston, TX 77030, USA
Brain Res Mol Brain Res 120:91-102. 2004..Thus, nicotinic stimulation produces a transcription-dependent increase in TH mRNA half-life that is mediated by previously unrecognized TH mRNA binding proteins...
- The multimeric nonstructural NS2 proteins of bluetongue virus, African horsesickness virus, and epizootic hemorrhagic disease virus differ in their single-stranded RNA-binding abilityJ M Uitenweerde
Department of Genetics, University of Pretoria, South Africa
Virology 209:624-32. 1995..The ability of the NS2 proteins to form virus inclusion body-like structures in baculovirus-infected cells is not affected by the ssRNA-binding disparity...
- The KRAB zinc finger gene ZNF74 encodes an RNA-binding protein tightly associated with the nuclear matrixB Grondin
Institut de Recherches Cliniques de Montreal, Universite de Montreal, Montreal, Quebec H2W 1R7, Canada
J Biol Chem 271:15458-67. 1996..The RNA binding properties of this protein and its tight association with the nuclear matrix, a subnuclear compartment involved in DNA replication as well as RNA synthesis and processing, suggest a role for ZNF74 in RNA metabolism...
- Interaction of antimalarial drug quinacrine with nucleic acids of variable sequence studied by spectroscopic methodsL Rivas
Instituto de Estructura de la Materia, CSIC, Serrano, Madrid, Spain
J Biomol Struct Dyn 18:371-83. 2000..The interaction of QA with the above nucleic acids lead to a different change in the chain stability and flexibility which is further related to the different denaturation tendency of the polymer in the presence of the metal surface...
- Protein-primed and de novo initiation of RNA synthesis by norovirus 3DpolJacques Rohayem
Institut fur Virologie, The Calicilab, Fiedlerstrasse 42, D 01307 Dresden, Germany
J Virol 80:7060-9. 2006..We propose a novel model for initiation of replication of the norovirus genome by 3D(pol), with a VPg-protein-primed initiation of replication of polyadenylated genomic RNA and a de novo initiation of replication of antigenomic RNA...
- An RNA helicase, DDX1, interacting with poly(A) RNA and heterogeneous nuclear ribonucleoprotein KHui Chin Chen
Institute of Molecular Medicine, College of Medicine, National Taiwan University, Academia Sinica, No 1 Sec 4, Roosevelt Road, Taipei 106, Taiwan
J Biol Chem 277:40403-9. 2002..Moreover, the immunoprecipitated DDX1 complex but not purified DDX1 can unwind double-stranded RNA having single-stranded poly(A) overhangs...
- Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylaseSarah L Zimmer
Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, NY 14853, USA
Plant J 59:88-99. 2009..Together, our results identify several Ntr-PAPs and PNPase in organelle polyadenylation, and reveal novel poly(U)-rich sequences in Chlamydomonas mitochondria...
- Structural and functional studies of the rat mitochondrial single strand DNA binding protein P16G D Hoke
Department of Biochemistry and Molecular Biophysics, Virginia Commonwealth University, Richmond 23298
Arch Biochem Biophys 282:116-24. 1990..Furthermore, the amino-terminal sequence was found to be strikingly similar to that of the Xenopus laevis mtSSB-1 and to a lesser extent similar to E. coli SSB and E. coli F sex factor SSB...
- Recombinant dengue virus type 1 NS3 protein exhibits specific viral RNA binding and NTPase activity regulated by the NS5 proteinT Cui
Institute of Molecular and Cell Biology, National University of Singapore, Republic of Singapore
Virology 246:409-17. 1998..These data suggest that the NTPase activity of the NS3 protein may be regulated by the viral NS5 protein during virus replication...
- Kinetics of inhibition of rabbit reticulocyte peptidyltransferase by anisomycin and sparsomycinM Ioannou
Laboratory of Biochemistry, School of Medicine, University of Patras, 26110 Patras, Greece
Mol Pharmacol 53:1089-96. 1998..During this phase, AcPhe-puromycin is produced from a new, modified ribosomal complex with a lower catalytic rate constant. Thus, sparsomycin also acts as a modifier of eukaryotic peptidyltransferase activity...
- The existence of eukaryotic ribonucleoprotein consensus sequence-type RNA-binding proteins in a prokaryote, Synechococcus 6301M Sugita
Center for Gene Research, Nagoya University, Japan
Nucleic Acids Res 22:25-31. 1994..Due to the easiness of genetic manipulations the cyanobacterium will provide an excellent system to analyze the function of not only cyanobacterial but also plant RNA-binding proteins...
- The A26G replacement in the consensus sequence A-X-X-X-X-G-K-[T,S] of the guanine nucleotide binding site activates the intrinsic GTPase of the elongation factor 2 from the archaeon Sulfolobus solfataricusE De Vendittis
Dipartimento dei Biochimica e Biotecnologie Mediche, , II, Italy
Eur J Biochem 262:600-5. 1999..These findings suggest that A26 is a regulator of the biochemical functions of SsEF-2. The involvement of this alanine residue in the guanine nucleotide-binding pocket of EF-2 or EF-G is discussed...
- Small molecule-RNA interaction: spectroscopic and calorimetric studies on the binding by the cytotoxic protoberberine alkaloid coralyne to single stranded polyribonucleotidesMaidul Islam
Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S C Mullick Road, Kolkata 700032, India
Biochim Biophys Acta 1790:829-39. 2009..This study is aimed to elucidate the specificity of the alkaloid coralyne to poly(G), poly(C), poly(I) and poly(U) in the light of its ability in inducing self-structure in poly(A)...
- Polyadenylic: polyuridylic acid-induced determinants of host resistance to cytomegalovirus and their potentiation by hyperthermiaB K Lee
Department of Medical Microbiology and Immunology, University of Minnesota, Duluth 55812 2487
J Immunother (1991) 12:105-14. 1992The ability of spleen cells from poly A:poly U-treated mice to inhibit murine cytomegalovirus (MCMV) replication in confluent monolayer cells of secondary mouse embryo fibroblasts (MEFs) cultured at 37 and 40 degrees C was investigated...
- A distinctive ribonuclease from fresh fruiting bodies of the medicinal mushroom Ganoderma lucidumH X Wang
Department of Microbiology, College of Biological Science, China Agricultural University, Beijing, China
Biochem Biophys Res Commun 314:519-22. 2004..A pH of 4.0 and a temperature of 60 degrees C were required for optimal activity of the enzyme. The optimum pH was low compared with those reported for other mushroom ribonucleases...
- Altered degradation of circulating nucleic acids and oligonucleotides in diabetic patientsG Kocic
Institute of Biochemistry, Medical Faculty University of Nis, Serbia
Diabetes Res Clin Pract 79:204-13. 2008..Decreased RNase activity and related increase of circulating oligonucleotides may favor the increase of nucleic acid "danger motifs", leading to TLRs activation...
- Polyadenylation proteins CstF-64 and tauCstF-64 exhibit differential binding affinities for RNA polymersRoberto R Monarez
Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
Biochem J 401:651-8. 2007..This supports the hypothesis that tauCstF-64 promotes germ-cell-specific patterns of polyadenylation by binding to different downstream sequence elements...
- The formation of phosphate end groups in the radiolysis of polynucleotides in aqueous solutionC P Murthy
, Bundesrepublik Deutschland
Z Naturforsch C 43:572-6. 1988..This is possibly linked to the decomposition of unstable hydroperoxides which are formed in high yields in poly(U) and poly(C) (G = 0.7 and 0.19 mumol J-1, resp.).(ABSTRACT TRUNCATED AT 250 WORDS)..
- RNA synthetic activity of glutamate dehydrogenase: determination of enzyme purity, RNA characteristics, and deamination/amination ratioGodson O Osuji
Cooperative Agricultural Research Center, Prairie View A and M University, Texas A and M University System, PO Box 4079, Prairie View, TX 77446, USA
Appl Biochem Biotechnol 119:209-28. 2004....
- A 20-amino-acid autonomous RNA-binding domain contained in an enoyl-CoA hydrataseJ Nakagawa
Institute for Medical Microbiology, University of Basel, Switzerland
Eur J Biochem 244:890-9. 1997..By contrast, the hydratase activity of AUH required an intact three-dimensional conformation, as most mutations downstream of Ser68 impaired enzymatic activity...
- Kinetic studies on the interaction between a ribosomal complex active in peptide bond formation and the macrolide antibiotics tylosin and erythromycinG P Dinos
Laboratory of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
Biochemistry 39:11621-8. 2000..The determination of K(er), k(6), and k(7) enables us to classify erythromycin as a slow-binding ligand of ribosomes...
- Characterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependenceS Yehudai-Resheff
Department of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
Nucleic Acids Res 28:1139-44. 2000..However, RNA 3'-ends produced by endonucleolytic cleavage by RNase E in single-strand regions of mRNA molecules may serve as efficient substrates for polyadenylation that direct these molecules for rapid exonucleolytic degradation...
- Biochemical characterization of the equine arteritis virus helicase suggests a close functional relationship between arterivirus and coronavirus helicasesA Seybert
Institute of Virology and Immunology, University of Wurzburg, Wurzburg, Germany
J Virol 74:9586-93. 2000..Thus, the combined data strongly support the idea that nidovirus helicases may represent a separate group of RNA virus-encoded helicases with distinct properties...
- Changes in ribosomal activity of Escherichia coli cells during prolonged culture in sea salts mediumD L Kalpaxis
Laboratory of Biochemistry, School of Medicine, University of Patras, Greece
J Bacteriol 180:3114-9. 1998..An analogous effect of reconstitution on the efficiency of ribosomes in binding AcPhe-tRNA was evident not only during the initial phase but throughout the starvation period...
- Polysaccharide--polynucleotide complexes. 2. Complementary polynucleotide mimic behavior of the natural polysaccharide schizophyllan in the macromolecular complex with single-stranded RNA and DNAK Sakurai
Organization and Function, PRESTO and Chemotransfiguration Project, Japan Science and Technology Corporation JST, Kurume Research Center Building, 2432 Aikawa, Kurume, Fukuoka 839 0861, Japan
Biomacromolecules 2:641-50. 2001..Furthermore, stoichiometric study suggested that the complex structure is a triple helix consisting of two s-SPG and one poly(C) or poly(A) chains...
- The EWS gene, involved in Ewing family of tumors, malignant melanoma of soft parts and desmoplastic small round cell tumors, codes for an RNA binding protein with novel regulatory domainsT Ohno
Department of Microbiology and Immunology, Jefferson Cancer Institute, Philadelphia, PA 19107 5541
Oncogene 9:3087-97. 1994..The EWS-b protein binds to RNA in vitro and, specifically, to poly G and poly U. The RNA binding activity was localized to the carboxy terminal 86 amino acids, which constitute RGG box...
- Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitionsS G Nadler
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
Biochemistry 30:2968-76. 1991..abstract truncated at 250 words)..
- Properties of isolated domains of the elongation factor Tu from Thermus thermophilus HB8S Nock
, , Germany
Eur J Biochem 234:132-9. 1995..Interdomain interactions must be important for the stabilisation of the structure of domain I, since isolated T. thermophilus EF-TuI is thermolabile despite the presence of the 181-190 loop.(ABSTRACT TRUNCATED AT 250 WORDS)..
- De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virusG Luo
Department of Virology, Bristol Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut 06492 7660, USA
J Virol 74:851-63. 2000..These findings suggest that HCV NS5B is able to initiate RNA synthesis de novo...
- Expression, phosphorylation, and mRNA-binding of heterogeneous nuclear ribonucleoprotein K in Xenopus oocytes, eggs, and early embryosTetsushi Iwasaki
Research Center for Environmental Genomics, Kobe University, Kobe 657 8501, Japan
Dev Growth Differ 50:23-40. 2008..In vitro binding assay with the use of poly U monopolymeric RNA-coupled beads demonstrated that the RNA-binding property of hnRNP K is negatively regulated by ..
- Annexin A2 is a novel RNA-binding proteinNolan R Filipenko
Cancer Biology Research Group, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
J Biol Chem 279:8723-31. 2004..Transfection of LNCaP cells with the ANXA2 gene resulted in the up-regulation of c-Myc protein. These findings identify ANXA2 as a Ca(2+)-dependent RNA-binding protein that interacts with the mRNA of the nuclear oncogene, c-myc...
- Cis-acting RNA elements in hepatitis C virus replicationGuangxiang Luo; Fiscal Year: 2003..abstract_text> ..
- Cis-acting RNA elements in hepatitis C virus replicationGuangxiang Luo; Fiscal Year: 2007..abstract_text> ..
- Cis-acting RNA elements in hepatitis C virus replicationGuangxiang Luo; Fiscal Year: 2006..abstract_text> ..
- MECHANISMS OF CONTROL OF THE GAP-43 GENENora Perrone Bizzozero; Fiscal Year: 1999....
- HCV Genotype 6: A Model for HCV Genetics and Molecular Epidemiology StudiesLing Lu; Fiscal Year: 2010..This information and the derived models are vital for better strategies of HCV diagnosis and treatment, and the improved designs of antivirals and vaccines. ..
- The Nuclear Pore Complex: Interphase and Mitotic FunctionKatharine S Ullman; Fiscal Year: 2010..Such defects in morphology and DNA content are hallmarks of aggressive cancer cells, and the research proposed here will contribute to a better understanding of how these alterations arise. ..
- RNA Uridylytransferases of TrypanosomesRuslan Aphasizhev; Fiscal Year: 2007..Sequences of the newly identified UTP-specific transferases will be used to establish characteristic protein motifs for this family of enzymes. ..
- Function of 3'UTRsMARVIN P WICKENS; Fiscal Year: 2011..These proteins control stem cells and participate in the formation of memory. Understanding how they work should provide practical opportunities for intervention. ..
- CLEAVAGE, POLYADENYLATION, AND TRANSPORT OF MRNAMarvin Wickens; Fiscal Year: 2007..In focusing sharply on a few specific examples, we hope to illuminate the broad molecular questions of how 3'UTR controls function, evolve, and coordinate exoression of multiole mRNAs. ..
- Function of 3' UTRsMarvin Wickens; Fiscal Year: 2007..We focus sharply on PUF proteins to illuminate broadly how 3'UTR controls function, evolve, and coordinate expression of multiple mRNAs. ..
- The Role of HuR in mutant SOD1 dysregulation of VEGF mRNA ProcessingPeter H King; Fiscal Year: 2010..There is no cure for this disease or any mitigating therapy. This proposal will address a novel area of growth factor regulation that may contribute to the cause of this disease, and thus may ultimately lead to novel therapies. ..
- Aberrant VEGF RNA Stability in Amyotrophic Lateral SclerosisPeter King; Fiscal Year: 2007....
- The Nuclear Pore Complex: Interphase and Mitotic FunctionKATHARINE ULLMAN; Fiscal Year: 2007..The information gathered will impact practical applications, such as optimizing expression of exogenously introduced genes as well as understanding -and ultimately controlling-growth deregulation found in cancerous cells. ..
- The Role of HuR in mutant SOD1 dysregulation of VEGF mRNA ProcessingPeter H King; Fiscal Year: 2010..There is no cure for this disease or any mitigating therapy. This proposal will address a novel area of growth factor regulation that may contribute to the cause of this disease, and thus may ultimately lead to novel therapies. ..
- Function of 3'UTRsMARVIN P WICKENS; Fiscal Year: 2010..These proteins control stem cells and participate in the formation of memory. Understanding how they work should provide practical opportunities for intervention. ..
- Regulation of Lung Epithelial Fibrinolysis by UrokinaseSreerama Shetty; Fiscal Year: 2005..This information could hasten the development of new, mechanism-based interventions for lung disorders, including acute lung injury or lung neoplasia. ..
- FUNCTION OF 3 UTRSMarvin Wickens; Fiscal Year: 2002..Our detailed investigations of the regulation of c-mos, a proto-oncogene normally expressed only in the germ line, bear on how cell division is controlled both in normal and abnormal growth. ..
- MOLECULAR MECHANISMS OF NUCLEAR EXPORTKATHARINE ULLMAN; Fiscal Year: 2004..Through genetic and biochemical interaction analyses, Nup153 will be used to construct a bigger picture of key connections made between export machinery components. ..
- The Role of HuR in mutant SOD1 dysregulation of VEGF mRNA ProcessingPeter King; Fiscal Year: 2009..There is no cure for this disease or any mitigating therapy. This proposal will address a novel area of growth factor regulation that may contribute to the cause of this disease, and thus may ultimately lead to novel therapies. ..
- CONTROL OF FIBRINOLYTIC PATHWAYS IN LUNG DISEASESreerama Shetty; Fiscal Year: 2002..This work may suggest new therapeutic approaches to a variety of inflammatory or neoplastic lung diseases for which current therapy is often unsatisfactory. ..
- RNA Uridylytransferases of TrypanosomesRuslan Aphasizhev; Fiscal Year: 2009..Sequences of the newly identified UTP-specific transferases will be used to establish characteristic protein motifs for this family of enzymes. ..
- Structures and Functions of RNA Editing TUTasesRuslan Aphasizhev; Fiscal Year: 2011..Targeting essential parasite-specific enzymes, such as mitochondrial RNA editing terminal uridylyl transferases (TUTases), is a promising approach toward a new generation of trypanocides. ..