transfer rna

Summary

Summary: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.

Top Publications

  1. pmc ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
    Dean Laslett
    Murdoch University, Perth, Western Australia, Australia
    Nucleic Acids Res 32:11-6. 2004
  2. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
  3. pmc GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    Patricia P Chan
    Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE 2, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 37:D93-7. 2009
  4. pmc Solving the riddle of codon usage preferences: a test for translational selection
    Mario dos Reis
    School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
    Nucleic Acids Res 32:5036-44. 2004
  5. ncbi ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences
    Dean Laslett
    Murdoch University, Perth, Western Australia, Australia
    Bioinformatics 24:172-5. 2008
  6. ncbi Evolution of mitochondrial gene content: gene loss and transfer to the nucleus
    Keith L Adams
    Department of Botany, Iowa State University, 353 Bessey Hall, Ames, IA 50011, USA
    Mol Phylogenet Evol 29:380-95. 2003
  7. ncbi tRNA's wobble decoding of the genome: 40 years of modification
    Paul F Agris
    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 7622, USA
    J Mol Biol 366:1-13. 2007
  8. ncbi Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
  9. ncbi Structure of the 70S ribosome complexed with mRNA and tRNA
    Maria Selmer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 313:1935-42. 2006
  10. ncbi The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths
    Stephen L Cameron
    Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, Canberra, ACT, Australia
    Gene 408:112-23. 2008

Research Grants

  1. Structure and function of SRP RNA
    Christian Zwieb; Fiscal Year: 2006
  2. CRYSTALLOGRAPHIC STUDIES ON RIBOSOMAL PARTICLES
    ADA E YONATH; Fiscal Year: 2010
  3. Maintenance of the tRNA 3' end
    Ya Ming Hou; Fiscal Year: 2008
  4. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2006
  5. Biochemical Genomics Linking Genes and Activities
    Eric Phizicky; Fiscal Year: 2004
  6. ENZYME MEDIATED THIOL MODIFICATION OF TRNA
    CHARLES LAUHON; Fiscal Year: 2002
  7. FUNCTIONAL ANALYSIS OF AN RNA STRUCTURAL MOTIF
    Ya Ming Hou; Fiscal Year: 2005
  8. RNA Transport Within the Nucleus
    Thoru Pederson; Fiscal Year: 2005
  9. RNA PROCESSING AND RIBONUCLEOPROTEIN
    Thoru Pederson; Fiscal Year: 2001
  10. A Study of Site-Specifically Modified RNAs
    Christine Chow; Fiscal Year: 2006

Detail Information

Publications276 found, 100 shown here

  1. pmc ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
    Dean Laslett
    Murdoch University, Perth, Western Australia, Australia
    Nucleic Acids Res 32:11-6. 2004
    ..The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags...
  2. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
    ..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
  3. pmc GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    Patricia P Chan
    Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE 2, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 37:D93-7. 2009
    ..The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu...
  4. pmc Solving the riddle of codon usage preferences: a test for translational selection
    Mario dos Reis
    School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
    Nucleic Acids Res 32:5036-44. 2004
    ..Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model...
  5. ncbi ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences
    Dean Laslett
    Murdoch University, Perth, Western Australia, Australia
    Bioinformatics 24:172-5. 2008
    ..This is one of the reasons why current tRNA gene predictor programs perform poorly identifying mitochondrial tRNA genes. As a consequence there is a need for a new program with the specific aim of predicting these tRNAs...
  6. ncbi Evolution of mitochondrial gene content: gene loss and transfer to the nucleus
    Keith L Adams
    Department of Botany, Iowa State University, 353 Bessey Hall, Ames, IA 50011, USA
    Mol Phylogenet Evol 29:380-95. 2003
    ..Several hypotheses have been proposed for why mitochondrial genes are transferred to the nucleus, why mitochondria retain genomes, and why functional gene transfer is almost exclusively unidirectional...
  7. ncbi tRNA's wobble decoding of the genome: 40 years of modification
    Paul F Agris
    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 7622, USA
    J Mol Biol 366:1-13. 2007
    ....
  8. ncbi Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
    Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3...
  9. ncbi Structure of the 70S ribosome complexed with mRNA and tRNA
    Maria Selmer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 313:1935-42. 2006
    ..8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA)...
  10. ncbi The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths
    Stephen L Cameron
    Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, Canberra, ACT, Australia
    Gene 408:112-23. 2008
    ....
  11. pmc Universal rules and idiosyncratic features in tRNA identity
    R Giege
    Unite Propre de Recherche 9002, Structure des Macromolecules Biologiques et Mecanismes de Reconnaissance, Scientifique, 15 rue Rene Descartes, F 67084, Strasbourg Cedex, France
    Nucleic Acids Res 26:5017-35. 1998
    ..Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities...
  12. pmc Nuclear processing and export of microRNAs in Arabidopsis
    Mee Yeon Park
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Proc Natl Acad Sci U S A 102:3691-6. 2005
    ..These results demonstrate that HST and PSD do not share RNA cargos in nuclear export and strongly suggest that there are multiple nuclear export pathways for these small RNAs in Arabidopsis...
  13. ncbi Genome evolution in yeasts
    Bernard Dujon
    Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
    Nature 430:35-44. 2004
    ....
  14. pmc The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    Jamie J Cannone
    Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712 1095, USA
    BMC Bioinformatics 3:2. 2002
    ..This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields...
  15. ncbi Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 34:273-83. 2005
    ..Given the paraphyletic nature of ascidians, it seems likely that the common ancestor of ascidians and thaliaceans was sessile, as are the present-day ascidians, and that the thaliaceans subsequently evolved a pelagic lifestyle...
  16. ncbi Isolation and characterization of the putative nuclear modifier gene MTO1 involved in the pathogenesis of deafness-associated mitochondrial 12 S rRNA A1555G mutation
    Xiaoming Li
    Division of Human Genetics, Children s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
    J Biol Chem 277:27256-64. 2002
    ..These observations suggest that human MTO1 is a structural and functional homolog of yeast MTO1. Thus, it may play an important role in the pathogenesis of deafness-associated A1555G mutation in 12 S rRNA gene or mutations in tRNA genes...
  17. pmc tRNA cleavage is a conserved response to oxidative stress in eukaryotes
    Debrah M Thompson
    Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
    RNA 14:2095-103. 2008
    ..Similar tRNA fragments are also observed in human cell lines and in plants during oxidative stress. These results demonstrate that tRNA cleavage is a conserved aspect of the response to oxidative stress...
  18. ncbi Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage
    Paul G Higgs
    Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 25:2279-91. 2008
    ..We analyze a set of 80 complete bacterial genomes and show that the theory predicts many of the trends that are seen in these data...
  19. ncbi Selective charging of tRNA isoacceptors explains patterns of codon usage
    Johan Elf
    Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 751 24 Uppsala, Sweden
    Science 300:1718-22. 2003
    ....
  20. pmc Insights into translational termination from the structure of RF2 bound to the ribosome
    Albert Weixlbaumer
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Science 322:953-6. 2008
    ..by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3...
  21. pmc Post-transcriptional nucleotide modification and alternative folding of RNA
    Mark Helm
    Department of Chemistry, Institute for Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D 69120 Heidelberg, Germany
    Nucleic Acids Res 34:721-33. 2006
    ..In this paper, functional, genomic and structural evidence on cases of folding space alteration by post-transcriptional modifications in native RNA are reviewed...
  22. ncbi The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea)
    Min Hu
    Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Victoria 3030, Werribee, Australia
    Int J Parasitol 32:145-58. 2002
    ..Both hookworm genomes encode 12 protein, two ribosomal RNA and 22 transfer RNA genes, but lack the ATP synthetase subunit 8 gene, which is consistent with three other species of Secernentea ..
  23. ncbi Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome
    M V Rodnina
    Institute of Molecular Biology, University of Witten Herdecke, Germany
    Nature 385:37-41. 1997
    ..By coupling the free energy of GTP hydrolysis to translocation, EF-G serves as a motor protein to drive the directional movement of transfer and messenger RNAs on the ribosome...
  24. ncbi Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions
    Yoshiho Ikeuchi
    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8656, Japan
    Mol Cell 21:97-108. 2006
    ....
  25. pmc Improvement of reading frame maintenance is a common function for several tRNA modifications
    J Urbonavicius
    Department of Microbiology, Umea University, S 90 187 Umeå, Sweden
    EMBO J 20:4863-73. 2001
    ..We propose that the improvement of reading frame maintenance has been and is the major selective factor for the emergence of new modified nucleosides...
  26. ncbi Structural basis for translation termination on the 70S ribosome
    Martin Laurberg
    Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Nature 454:852-7. 2008
    At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon...
  27. pmc The frequency of translational misreading errors in E. coli is largely determined by tRNA competition
    Emily B Kramer
    Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland, Baltimore, Maryland 21250, USA
    RNA 13:87-96. 2007
    ....
  28. ncbi Stress induces tRNA cleavage by angiogenin in mammalian cells
    Hanjiang Fu
    Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People s Republic of China
    FEBS Lett 583:437-42. 2009
    ..These results imply that angiogenin plays an important physiological role in cell stress response, except for the known function of inducing angiogenesis...
  29. pmc Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation
    Takashi P Satoh
    Collection Center, National Museum of Nature and Science, 3 23 1 Hyakunincho, Shinjuku ku, Tokyo 169 0073, Japan
    BMC Genomics 11:479. 2010
    ..It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order...
  30. pmc The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum
    R Okimoto
    Department of Biology, University of Utah, Salt Lake City 84112
    Genetics 130:471-98. 1992
    ..elegans and A. suum ancestral lines diverged close to the time of divergence of the cow and human ancestral lines, about 80 million years ago...
  31. ncbi An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation
    Andreas Savelsbergh
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    Mol Cell 11:1517-23. 2003
    ..These results indicate that the energy of GTP hydrolysis is utilized to promote the ribosome rearrangement and to bias spontaneous fluctuations within the ribosome-EF-G complex toward unidirectional movement of mRNA and tRNA...
  32. pmc The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae)
    Paola Salvato
    Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Agripolis, Viale dell Universita 16, 35020 Legnaro, Italy
    BMC Genomics 9:331. 2008
    ..Thus advance of lepidopteran mitogenomics deeply requires new genomes derived from a broad taxon sampling. In present work we describe the mitochondrial genome of the moth Ochrogaster lunifer...
  33. ncbi The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs
    Susan E Masta
    Department of Energy Joint Genome Institute, Department of Evolutionary Genomics, Walnut Creek, California, USA
    Mol Biol Evol 21:893-902. 2004
    ..Most of the transfer RNA (tRNA) gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary ..
  34. ncbi Drosophila melanogaster mitochondrial DNA: completion of the nucleotide sequence and evolutionary comparisons
    D L Lewis
    Department of Biochemistry, Michigan State University, East Lansing, USA
    Insect Mol Biol 4:263-78. 1995
    ..yakuba mtDNA. All genes encoded in the mtDNA of both species are in identical locations and orientations. Nucleotide substitution analysis reveals that tRNA and rRNA genes evolve at less than half the rate of protein coding genes...
  35. pmc Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    Genome Res 14:2279-86. 2004
    ..It also provides new evidence that a selective force for the optimization of the translation machinery is the maximization of growth...
  36. ncbi Selection of tRNA by the ribosome requires a transition from an open to a closed form
    James M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom
    Cell 111:721-32. 2002
    ..We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity...
  37. pmc Regulatory RNAs derived from transfer RNA?
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    RNA 16:1865-9. 2010
    ..If their regulatory functions were to be confirmed, these newly revealed RNAs would add to the expanding repertoire of small noncoding RNAs and would also provide new perspectives on the coevolution of transfer RNA and messenger RNA.
  38. ncbi Crystal structure of the ribosome at 5.5 A resolution
    M M Yusupov
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Science 292:883-96. 2001
    ..The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement...
  39. ncbi The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects
    C B Beard
    Centers for Disease Control and Prevention, Public Health Service, US Department of Health and Human Services, Atlanta, GA 30314 3724, USA
    Insect Mol Biol 2:103-24. 1993
    ..Comparisons were made with the mitochondrial genomes of other insects on the basis genome size and organization, DNA and putative amino acid sequence data, nucleotide substitutions, codon usage and bias, and patterns of AT enrichment...
  40. pmc An early step in wobble uridine tRNA modification requires the Elongator complex
    Bo Huang
    Department of Molecular Biology, Umea University, 901 87 Umea, Sweden
    RNA 11:424-36. 2005
    ..b>Transfer RNA immunoprecipitation experiments showed that the Elp1 and Elp3 proteins specifically coprecipitate a tRNA ..
  41. pmc The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization
    R H Crozier
    Department of Genetics and Human Variation, La Trobe University, Bundoora, Victoria, Australia
    Genetics 133:97-117. 1993
    ....
  42. ncbi Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes
    K H Wolfe
    Department of Biology, Indiana University, Bloomington 47405
    J Mol Evol 35:304-17. 1992
    ..Despite the compactness and extensive gene loss, one translational gene (infA, encoding initiation factor 1) that is a pseudogene in tobacco has been maintained intact in Epifagus...
  43. pmc Angiogenin cleaves tRNA and promotes stress-induced translational repression
    Satoshi Yamasaki
    Division of Rheumatology, Immunology and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    J Cell Biol 185:35-42. 2009
    ..In this paper, we show that arsenite, heat shock, or ultraviolet irradiation promotes transfer RNA (tRNA) cleavage and accumulation of tRNA-derived, stress-induced small RNAs (tiRNAs)...
  44. pmc Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans
    D V Lavrov
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    Genetics 157:621-37. 2001
    ..The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level...
  45. pmc Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnicalis
    Brad S Coates
    USDA ARS, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, c o Insectary, Iowa State University, Ames, Iowa, 50011
    Int J Biol Sci 1:13-8. 2005
    ..2%) compared to 2-fold degenerate codons (2.6%). These are the 3(rd) and 4(th) lepidopteran mitochondrial genome reference sequences in GenBank and useful for comparative mitochondrial studies...
  46. pmc Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia
    Yan Li
    Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Zhongshan University, Guangzhou 510275, P R China
    Nucleic Acids Res 36:6048-55. 2008
    ..Our results may provide new insight into a novel mechanism for stressed G. lamblia to regulate gene expression globally...
  47. ncbi Cell-free translation reconstituted with purified components
    Y Shimizu
    Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bldg FSB401, Kasiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan
    Nat Biotechnol 19:751-5. 2001
    ..Moreover, omission of a release factor allowed efficient incorporation of an unnatural amino acid using suppressor transfer RNA (tRNA).
  48. pmc Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations
    Min Xin Guan
    Division and Program in Human Genetics, Cincinnati Children s Hospital Medical Center, Cincinnati, Ohio 45229 3039, USA
    Am J Hum Genet 79:291-302. 2006
    ..we identified the nuclear-modifier gene TRMU, which encodes a highly conserved mitochondrial protein related to transfer RNA (tRNA) modification...
  49. ncbi Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup
    J W Ballard
    The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605 2496, USA
    J Mol Evol 51:48-63. 2000
    ..These data show the potential for comparative genomics to tease apart subtle forces that shape the evolution of DNA...
  50. ncbi Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA
    Sebastian Leidel
    Institute of Biochemistry, ETH Zurich, Schafmattstrasse 18, CH 8093 Zurich, Switzerland
    Nature 458:228-32. 2009
    ..Here we show that Urm1p, the most ancient UBL, acts as a sulphur carrier in the process of eukaryotic transfer RNA (tRNA) modification, providing a possible evolutionary link between UBL and sulphur transfer...
  51. pmc Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea
    Kosuke Fujishima
    Institute for Advanced Biosciences, Keio University, Tsuruoka 997 0017, Japan
    Proc Natl Acad Sci U S A 106:2683-7. 2009
    b>Transfer RNA (tRNA) is essential for decoding the genome sequence into proteins. In Archaea, previous studies have revealed unique multiple intron-containing tRNAs and tRNAs that are encoded on 2 separate genes, so-called split tRNAs...
  52. ncbi The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code
    D O Clary
    J Mol Evol 22:252-71. 1985
    ..Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in the D. yakuba mtDNA molecule where these nucleotides are compatible with function...
  53. ncbi Yeast Nfs1p is involved in thio-modification of both mitochondrial and cytoplasmic tRNAs
    Yumi Nakai
    Department of Biochemistry, Osaka Medical College, 2 7 Daigaku machi, Takatsuki, Osaka 569 8686, Japan
    J Biol Chem 279:12363-8. 2004
    ..These results suggest that Nfs1p is involved in the 2-thio-modification of both 5-carboxymethylaminomethyl-2-thiouridine in mt-tRNAs and mcm(5)s(2)U in cy-tRNAs...
  54. ncbi Structure and organization of the mitochondrial genome of the canine heartworm, Dirofilaria immitis
    M Hu
    Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
    Parasitology 127:37-51. 2003
    ..Irrespective of transpositions of transfer RNA (trn) genes and the non-coding, AT-rich region, there are 4 gene- or gene block-translocations between the mt ..
  55. pmc Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
    Kulwadee Phannachet
    Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
    Nucleic Acids Res 32:1422-9. 2004
    ..55 synthase (Psi55S) catalyzes isomerization of uridine (U) to pseudouridine (Psi) at position 55 in transfer RNA. The crystal structures of Thermotoga maritima Psi55S, and its complex with RNA, have been determined at 2...
  56. ncbi Biosynthesis of cytokinins
    Tatsuo Kakimoto
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    J Plant Res 116:233-9. 2003
    ..The isopentenylated side chain is hydroxylated to form zeatin-type cytokinins. An alternative pathway, in which a hydroxylated side chain is directly added to the N(6) position of the adenine moiety, has also been suggested...
  57. ncbi Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA
    Gayathri Srinivasan
    Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
    Science 296:1459-62. 2002
    ..Near a methyltransferase gene cluster is the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon...
  58. ncbi Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation
    Frank Peske
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    J Mol Biol 343:1183-94. 2004
    ....
  59. pmc Requirement for IscS in biosynthesis of all thionucleosides in Escherichia coli
    Charles T Lauhon
    School of Pharmacy, University of Wisconsin, Madison 53705, USA
    J Bacteriol 184:6820-9. 2002
    ..This may be due to a residual level of Fe-S cluster biosynthesis in iscS deletion strains. An overall scheme for thionucleoside biosynthesis in E. coli is discussed...
  60. ncbi Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein
    Hervé Brulé
    Department of Microbiology and Immunology, Medical College of Virginia Campus of Virginia Commonwealth University, Institute for Structural Biology and Drug Discovery, 800 East Leigh Street, Suite 212, Richmond, Virginia 23298, USA
    Biochemistry 43:9243-55. 2004
    ..Bioinformatic analysis of the human TRM5 genomic locus (KIAA1393) have identified TRM5 homologues in eukaryotes and archaea; however, no significantly homologous regions were identified in any prokaryotes including the TrmD gene...
  61. ncbi Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications
    VALERIE DE CRECY-LAGARD
    Department of Microbiology, University of Florida, Gainesville 32611 0700, USA
    IUBMB Life 59:634-58. 2007
    ....
  62. ncbi Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint
    Ata Ghavidel
    Ontario Cancer Institute, Division of Signaling Biology, Toronto, Ontario M5G 1L7, Canada
    Cell 131:915-26. 2007
    ....
  63. ncbi Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA
    S Noguchi
    J Biol Chem 257:6544-50. 1982
    ..coli for survival in the natural environment...
  64. pmc Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui
    Caroline Köhrer
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    RNA 14:117-26. 2008
    ..marismortui provide the tools necessary for experimentally confirming the presence of any tRNA in a cell and, thereby, to test computational predictions of tRNA genes...
  65. pmc Reverse translocation of tRNA in the ribosome
    Shinichiro Shoji
    Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
    Mol Cell 24:931-42. 2006
    ..e., direct movement of the tRNAs from the E and P sites to the P and A sites, respectively). These findings have important implications for the energetics of translocation...
  66. ncbi Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster
    Y Kumazawa
    Department of Earth and Planetary Sciences, Nagoya University, Japan
    Mol Biol Evol 13:1242-54. 1996
    ..The secondary structures of the determined tRNA genes point to the operation of simplification pressure on the T psi C arm of snake mitochondrial tRNAs...
  67. pmc Differential annotation of tRNA genes with anticodon CAT in bacterial genomes
    Francisco J Silva
    Departament de Genetica, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat 22085, 46071 Valencia, Spain
    Nucleic Acids Res 34:6015-22. 2006
    ..The acquisition of a tRNA(Ile) (TAT) gene by Mycoplasma mobile has led to the loss of both the tRNA(Ile) (CAT) and the tilS genes. The new tRNA has appropriated the function of decoding AUA codons...
  68. ncbi Deletion of a conserved, central ribosomal intersubunit RNA bridge
    Iraj K Ali
    Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Mol Cell 23:865-74. 2006
    ..However, Deltah69 50S subunits are unable to associate with 30S subunits in the absence of tRNA, are defective in RF1-catalyzed peptide release, and can be recycled in the absence of RRF...
  69. pmc Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases
    S Cusack
    European Molecular Biology Laboratory, Grenoble, France
    Nucleic Acids Res 19:3489-98. 1991
    ....
  70. ncbi Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA
    Martine Roovers
    Institut de Recherches Microbiologiques Jean Marie Wiame, B 1070 Bruxelles, Belgium
    Proteins 71:2076-85. 2008
    ..Interestingly, the N-terminal domain is capable of independent folding, while the isolated C-terminal domain is incapable of folding on its own, a situation similar to the one reported recently for the rRNA modification enzyme RsmC...
  71. pmc Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome
    Kevin G McGarry
    Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
    Mol Cell 20:613-22. 2005
    ..The effects of G2252U are suppressed by C2394A, further implicating the P/E state in mRNA destabilization. This work uncovers a functional attribute of the P/E state crucial for understanding translation...
  72. ncbi Structures of the bacterial ribosome at 3.5 A resolution
    Barbara S Schuwirth
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 310:827-34. 2005
    ....
  73. ncbi An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes
    Malisa Carullo
    Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
    J Mol Evol 66:484-93. 2008
    ..Our results suggest that the potential to suppress stop codons, the historical inertia, and the conflict between translation initiation and elongation can all contribute to determining the wobble nucleotide of tRNA anticodons...
  74. ncbi Four tRNA-like sequences and a serpin homologue encoded by murine gammaherpesvirus 68 are dispensable for lytic replication in vitro and latency in vivo
    J P Simas
    Department of Pathology, University of Cambridge, UK
    J Gen Virol 79:149-53. 1998
    ..In this study it is demonstrated that deletion of four of the tRNA-like sequences and ORF1 from the virus genome does not affect the ability of MHV-68 to replicate in vitro or to establish, and reactivate from, latency in vivo...
  75. pmc Crystal structure of a translation termination complex formed with release factor RF2
    Andrei Korostelev
    Center for Molecular Biology of RNA and Departments of Molecular, Cell and Developmental Biology and Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 105:19684-9. 2008
    ..We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis...
  76. ncbi Complete nucleotide sequence and organization of the mitogenome of the red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) and comparison with other lepidopteran insects
    Man Il Kim
    College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500 757, Korea
    Mol Cells 28:347-63. 2009
    ..However, the Geometroidea were unexpectedly identified as a sister group of the Bombycoidea, rather than the Papilionoidea...
  77. pmc A "gain of function" mutation in a protein mediates production of novel modified nucleosides
    Peng Chen
    Department of Molecular Biology, Umea University, S 901 87 Umea, Sweden
    EMBO J 24:1842-51. 2005
    ..The results are discussed in relation to the mechanism of reading frame maintenance and the evolution of modified nucleosides in tRNA...
  78. pmc Non-coding RNA annotation of the genome of Trichoplax adhaerens
    Jana Hertel
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D 04107 Leipzig, Germany
    Nucleic Acids Res 37:1602-15. 2009
    ..We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome...
  79. ncbi The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants
    Y Notsu
    Department of Genetic Diversity, National Institute of Agrobiological Sciences, Kannondai 2 1 2, Tsukuba, Ibaraki 305 8602, Japan
    Mol Genet Genomics 268:434-45. 2002
    ....
  80. pmc Transfer RNA processing in archaea: unusual pathways and enzymes
    Ilka U Heinemann
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    FEBS Lett 584:303-9. 2010
    b>Transfer RNA (tRNA) molecules are highly conserved in length, sequence and structure in order to be functional in the ribosome...
  81. pmc PAUSED, a putative exportin-t, acts pleiotropically in Arabidopsis development but is dispensable for viability
    Junjie Li
    Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
    Plant Physiol 132:1913-24. 2003
    ..In addition, a paused null allele, paused-6, is still viable, suggesting the presence of redundant tRNA export pathway(s) in Arabidopsis...
  82. ncbi Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit
    Jeffrey L Hansen
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    J Mol Biol 330:1061-75. 2003
    ..Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA...
  83. pmc Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications
    Paul F Agris
    Department of Molecular and Structural Biochemistry, 128 Polk Hall, Campus Box 7622, North Carolina State University, Raleigh, North Carolina 27695 7622, USA
    EMBO Rep 9:629-35. 2008
    ..For example, the modifications located within or adjacent to the anticodon of the transfer RNA (tRNA) enhance the accuracy of codon binding, maintain the translational reading frame and enable translocation ..
  84. ncbi Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life
    Hong Xue
    Department of Biochemistry and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China
    Gene 310:59-66. 2003
    ....
  85. ncbi Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain
    David G Waterman
    York Structural Biology Laboratory, University of York, Chemistry Department, York YO10 5YW, UK
    J Mol Biol 356:97-110. 2006
    ..The inaccessibility of U8 in the canonical L-shaped form of tRNA, and the existence of a glycine-rich linker joining the catalytic and RNA-binding moieties of ThiI suggest that structural changes may occur in both molecules upon binding...
  86. ncbi The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae)
    Ling Yang
    School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People s Republic of China
    Mol Biol Rep 36:1441-9. 2009
    ..The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, which confirmed that P. atrilineata is most closely related to the superfamily Bombycoidea...
  87. pmc TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase
    David H Ardell
    Department of Molecular Evolution, Evolutionary Biology Center Norbyvägen 18C Uppsala University SE 752 36 Uppsala Sweden
    Nucleic Acids Res 34:893-904. 2006
    ..Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity...
  88. ncbi Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution
    F Schluenzen
    Max Planck Research Unit for Ribosomal Structure, Hamburg, Germany
    Cell 102:615-23. 2000
    ..96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation...
  89. ncbi Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA
    Daryi Wang
    Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 24:2040-8. 2007
    ..Our observations support the proposition of Richly and Leister (2004) that "primary insertions of organellar DNAs are large and then diverge and fragment over evolutionary time."..
  90. ncbi A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting
    Olivier Namy
    Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Nature 441:244-7. 2006
    ..entrance channel, compromising the translocation process and leading to a spring-like deformation of the P-site transfer RNA. In addition, we identify movements of the likely eukaryotic ribosomal helicase and confirm a direct ..
  91. ncbi The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria
    Wenqi Ran
    Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 27:2129-40. 2010
    ....
  92. ncbi Codon bias as a factor in regulating expression via translation rate in the human genome
    Yizhar Lavner
    Department of Computer Science, Tel Hai Academic College, Upper Galilee 12210, Israel
    Gene 345:127-38. 2005
    ....
  93. pmc Sequence and comparative analysis of the maize NB mitochondrial genome
    Sandra W Clifton
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Plant Physiol 136:3486-503. 2004
    ..After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly three-fourths of the maize NB mitochondrial genome is still of unknown origin and function...
  94. ncbi Angiogenin is a cytotoxic, tRNA-specific ribonuclease in the RNase A superfamily
    S K Saxena
    Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
    J Biol Chem 267:21982-6. 1992
    ..One of these homologues purified from human eosinophils, eosinophil-derived neurotoxin, nonspecifically degrades oocyte RNA similar to RNase A and is also cytotoxic at very low concentrations...
  95. ncbi Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales
    Junichi Sugahara
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
    Mol Biol Evol 25:2709-16. 2008
    ..The sequences and secondary structures of the tRNA genes and their bulge-helix-bulge motifs were registered in SPLITSdb (http://splits.iab.keio.ac.jp/splitsdb/), a novel and comprehensive database for archaeal tRNA genes...
  96. ncbi Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities
    T G Hagervall
    J Biol Chem 262:8488-95. 1987
    ..The molecular activity of the methyltransferase activity (nm5s2U34----mnm5s2U34) is 74 min-1, and the steady state concentration of the enzyme is only 78 molecules/genome equivalent in cells growing at a specific growth rate of 1.0/h...
  97. pmc Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes
    Rodolfo García-Contreras
    Artie McFerrin Department of Chemical Engineering, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 3:e2394. 2008
    ..Therefore, Hha acts as a toxin in conjunction with co-transcribed YbaJ (TomB) that attenuates Hha toxicity...
  98. pmc The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae
    Debrah M Thompson
    Department of Molecular and Cellular Biology, and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA
    J Cell Biol 185:43-50. 2009
    ..Thus, detection of Rny1p, and possibly its orthologues, in the cytosol may be a conserved mechanism for assessing cellular damage and determining cell survival, analogous to the role of cytochrome c as a marker for mitochondrial damage...
  99. pmc Neogastropod phylogenetic relationships based on entire mitochondrial genomes
    Regina L Cunha
    Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales CSIC, 28006 Madrid, Spain
    BMC Evol Biol 9:210. 2009
    ..Neogastropoda has been classified into up to six superfamilies including Buccinoidea, Muricoidea, Olivoidea, Pseudolivoidea, Conoidea, and Cancellarioidea. Phylogenetic relationships among neogastropod superfamilies remain unresolved...
  100. pmc Tissue-specific differences in human transfer RNA expression
    Kimberly A Dittmar
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 2:e221. 2006
    Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge...
  101. pmc In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs
    Junichi Sugahara
    Institute for Advanced Biosciences, Keio University, Tsuruoka 997 0017, Japan
    RNA 13:671-81. 2007
    In archaeal species, several transfer RNA genes have been reported to contain endogenous introns...

Research Grants62

  1. Structure and function of SRP RNA
    Christian Zwieb; Fiscal Year: 2006
    ..These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function. [unreadable] [unreadable]..
  2. CRYSTALLOGRAPHIC STUDIES ON RIBOSOMAL PARTICLES
    ADA E YONATH; Fiscal Year: 2010
    ..These studies have already illuminated principles of drug selectivity, and provided significant basic knowledge of possible pathways of drug resistance, hence paving the way to improve therapeutic properties. ..
  3. Maintenance of the tRNA 3' end
    Ya Ming Hou; Fiscal Year: 2008
    DESCRIPTION (provided by applicant): All transfer RNA (tRNA) molecules contain a CCA sequence at the 3' end that is the site of amino acid attachment during decoding of genetic information, and is the site of initiation of primer ..
  4. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2006
    ..jannaschii to gain a broader insight into its aminoacyl-tRNA synthetases as a basis for understanding the origin and evolution of contemporary mRNA-encoded protein synthesis in extant organisms. [unreadable] [unreadable]..
  5. Biochemical Genomics Linking Genes and Activities
    Eric Phizicky; Fiscal Year: 2004
    ..Application of these techniques to other organisms, including humans and pathogens, will greatly accelerate biochemical analysis and can be used to rapidly identify drug targets. ..
  6. ENZYME MEDIATED THIOL MODIFICATION OF TRNA
    CHARLES LAUHON; Fiscal Year: 2002
    ....
  7. FUNCTIONAL ANALYSIS OF AN RNA STRUCTURAL MOTIF
    Ya Ming Hou; Fiscal Year: 2005
    ..coli CysRS for its ability to distinguish cysteine from serine. These studies shall shed new light on the molecular interactions responsible for the accurate translation of the genetic code. ..
  8. RNA Transport Within the Nucleus
    Thoru Pederson; Fiscal Year: 2005
    ..Another aspect of the project will address the intranuclear traffic of these RNAs in relation to proteins known to be involved in nuclear import or RNA export, i.e. the Ran-GTPase and TAP. ..
  9. RNA PROCESSING AND RIBONUCLEOPROTEIN
    Thoru Pederson; Fiscal Year: 2001
    ..The same studies should provide information on sequences required for nuclear export. These two inter-related projects test the hypothesis that the nucleolus is a more pluri-functional organelle than previously thought. ..
  10. A Study of Site-Specifically Modified RNAs
    Christine Chow; Fiscal Year: 2006
    ..abstract_text> ..
  11. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2006
    ..A final aim proposes a method for identifying the mRNA targets of regulatory RNAs (such as the newly discovered micro RNAs) by comparative genome analysis. ..
  12. Upgrade of X-Ray Diffractometers
    Peter Moore; Fiscal Year: 2005
    ..It is anticipated that this upgrade will significantly increase the rate at which structures are determined at Yale. ..
  13. Gene Duplication and Genome Evolution
    Austin Hughes; Fiscal Year: 2004
    ..5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome. ..
  14. PRINCIPLES OF SENSORY RECEPTION AND MOTOR FUNCTION
    Dieter Soll; Fiscal Year: 2006
    ..Finally, the assembly of complex biological structures is one of broad general interest. [unreadable] [unreadable]..
  15. STRUCTURE AND PHYSICAL PROPERTIES OF RNA
    Peter Moore; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  16. RIBOSOME STRUCTURE/FUNCTION
    Peter Moore; Fiscal Year: 2001
    ..The structures of all new crystals obtained that are suitable for crystallographic analysis will be pursued. Third, the crustal structure of elongation factor G (EF-G) complexed with a GTP analogue will be solved. ..
  17. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin L Hughes; Fiscal Year: 2010
    ..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
  18. EVOLUTION OF ESSENTIAL TRANSLATIONAL PATHWAYS IN ARCHAEA
    Dieter Soll; Fiscal Year: 2001
    ..A second unique feature of archael aminoacyl-tRNA formation is the use of enzymes distinct from any yet found in either eubacteria or eukaryotes to generate lysyl-tRNA and cysteinyl-tRNA. ..
  19. PURCHASE OF A MALDI-TOF MASS SPECTROMETER
    Christine Chow; Fiscal Year: 2002
    ..The CIF provides Ph.D.-level expertise in mass spectral techniques, and several in-house experts on mass spectrometry and MALDI-TOF will play key advisory roles. ..
  20. TMRNA AND TRANS TRANSLATION--MECHANISM AND BIOLOGY
    Kelly Williams; Fiscal Year: 2003
    ..5) Analyze structure of tmRNA alone and in trans-translation complexes by chemical probing, cross-linking, crystallographic, and electron micrographic (the latter two collaborative) approaches. ..
  21. REVERSE TRANSCRIPTASE AND OTHER HIV MOLECULAR STRUCTURES
    Thomas Steitz; Fiscal Year: 2002
    ..Crystallographic studies of both full length HIV integrase and the homologous transposase, TN552, complexed with suitable DNA substrates are aimed to produce mechanistic insights. ..
  22. NMR Console Upgrade and Cryoprobe
    Peter Moore; Fiscal Year: 2002
    ..There are several structural biology projects under consideration that demand this sensitivity because the molecules of interest aggregate at the concentrations required when standard probes are used. ..
  23. Small RNA therapeutics for AIDS-associated infection
    Fenyong Liu; Fiscal Year: 2010
    ..These results will facilitate the development of these novel RNA-based agents for treatment and studies of AIDS-associated opportunistic infections, including those caused by HCMV. ..
  24. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2006
    ..Such knowledge could help improve existing antibiotics and could also lead to the design of new ones. ..
  25. DNA REPLICATION AND GENE EXPRESSION OF CHLORELLA VIRUSES
    James Van Etten; Fiscal Year: 2009
    ..Thus, chlorella viruses are an important model for studying large nucleocytoplasmic dsDNA viruses because they have evolutionary ties to important mammalian viruses, such as the pox viruses and the quarantined African swine fever virus. ..
  26. Targeting a novel regulatory RNA with novel antibiotics
    Jennifer V Hines; Fiscal Year: 2010
    ....
  27. Chemical Basis for Potassium Channel Modulation
    PAMELA ENGLAND; Fiscal Year: 2006
    ..To determine the site(s) in HERG that interact with other proteins, photoreactive amino acids capable of forming protein cross-links will be site-specifically incorporated into the HERG. ..
  28. High throughput PCR assays for diagnosing tuberculosis
    Sanjay Tyagi; Fiscal Year: 2007
    ..abstract_text> ..
  29. Cytomegalovirus infection in oral cavity
    Fenyong Liu; Fiscal Year: 2009
    ..Understanding the mechanism of CMV infection in salivary gland will facilitate the development of novel strategies for treatment and prevention of CMV-associated oral diseases as well as viral systemic infections. ..
  30. Genetic Studies of African Anopheles Vectors of Malaria
    Jeffrey Powell; Fiscal Year: 2009
    ..Replacing natural vector populations with such strains require that the strain have high fitness. ..
  31. MOLECULAR ANALYSIS OF HIV1 REVERSE TRANSCRIPTION
    CASEY MORROW; Fiscal Year: 2008
    ..abstract_text> ..
  32. Quality Control of Protein Translation
    A Wali Karzai; Fiscal Year: 2008
    ..abstract_text> ..
  33. Acquisition of Xray Diffraction Instrumentation
    JOHN PERONA; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  34. Studies on start codon selection by eukaryotic ribosomes
    Katsura Asano; Fiscal Year: 2010
    ..gt;30 Ts- mutations mapping in rRNA obtained under an aim in the previous proposal will be used together with new mutations to be introduced at the predicted 40S subunit interface to mRNA. ..
  35. 2006 Thiol-based Redox Regulation and Signaling Gordon Research Conference
    VADIM GLADYSHEV; Fiscal Year: 2006
    ..A diverse mix of established and emerging leaders in the field, and of junior and senior investigators will be included in the program. [unreadable] [unreadable] [unreadable]..
  36. Selectivity determinants in DNA restriction and modification enzymes
    JOHN PERONA; Fiscal Year: 2009
    ..abstract_text> ..
  37. Nucleic Acids Gordon Research Conference
    SCOTT STROBEL; Fiscal Year: 2006
    ..Considerable time is allotted for discussion following formal lectures. Poster sessions and optional recreational activities will stimulate informal interactions. [unreadable] [unreadable] [unreadable] [unreadable]..
  38. CONTROL OF CELL GROWTH
    Jonathan Gallant; Fiscal Year: 2005
    ..Because starvation conditions and the occurrence of a hungry codon may be frequent in nature, these phenomena are important to an understanding of translation and its control. ..
  39. Oligonucleotides as Tools for Chemotherapy
    Paul Zamecnik; Fiscal Year: 2006
    ....
  40. MECHANISM OF INITIATION OF PROTEIN BIOSYNTHESIS
    JOHN HERSHEY; Fiscal Year: 2004
    ..The experiments will help elucidate the function and regulation of these key initiation factors. ..
  41. SURE (SUMMER UNDERGRADUATE RESEARCH EXPERIENCE) PROGRAM
    Christopher Francklyn; Fiscal Year: 2004
    ..abstract_text> ..
  42. INTEGRATIVE RESPONSES TO AMINO ACID DEFICIENCY
    Dorothy Gietzen; Fiscal Year: 2004
    ....
  43. IN VITRO EVOLUTION OF NEW MOLECULAR FUNCTIONS
    Jack Szostak; Fiscal Year: 2003
    ..The re-use of previously selected functions to evolve new functions will also be studied. The idea that proteins are better than RNA at evolving new functions from existing functions will also be tested. ..
  44. Redox mechanism of cancer prevention by selenium
    VADIM GLADYSHEV; Fiscal Year: 2002
    ..These approaches should yield insight into the mechanism of the anticancer effect of selenium and may lead to the identification of human cancers most susceptible to selenium chemoprevention. ..
  45. EXERCISE, LIPOLYSIS AND FAT OXIDATION
    Robert Wolfe; Fiscal Year: 2002
    ..abstract_text> ..
  46. EXERCISE EFFECTS ON PROTEIN METABOLISM
    Robert Wolfe; Fiscal Year: 2002
    ..The results of this study will also contribute to our understanding of the mechanism whereby nutritional intake affects muscle protein metabolism. ..
  47. X-Ray Crystallography Imaging Plate Detector
    Harry Noller; Fiscal Year: 2002
    ....
  48. SPLICEOSOME ASSEMBLY AND FUNCTION
    Alan Weiner; Fiscal Year: 2001
    ....
  49. Genetic Analysis of U5-PBS Role in HIV Neuropathogenesis
    CASEY MORROW; Fiscal Year: 2004
    ..abstract_text> ..
  50. CONSTRUCTION AND ANALYSIS OF RETROVIRUS MUTANTS
    Stephen Goff; Fiscal Year: 2003
    ..In each case, these tests will be applied to existing panels of mutants to help localize the regions needed for these activities. ..
  51. Brain Signaling of Essential Amino Acid Deficiency
    Dorothy Gietzen; Fiscal Year: 2006
    ..When APC neurons are activated, their glutamatergic output first acts at AMPA receptors to signal AA deficiency to other parts of the brain for the anorectic responses. ..
  52. Structure Function Studies of a RNA Antiterminator Bulge
    Jennifer Hines; Fiscal Year: 2005
    ..Specific Aim IV: She will begin to look at the effects small RNA binding ligands may have on the solution behavior of the antiterminator alone or complexed with tRNA acceptor stem. ..
  53. MATHEMATICAL TOOLS AND MODELING FOR BIOLOGISTS
    David Krakauer; Fiscal Year: 2005
    ..The proposal describes a series of short courses and workshops across both disciplines and details the plan for the first of three workshops that are concerned with issues at the interface of theoretical and experimental biology. ..
  54. Transcriptional Control of the E. coli Pap Operon
    JOHN PERONA; Fiscal Year: 2005
    ..Detailed information on pap regulation should thus be helpful in designing strategies to inhibit host colonization and pathogenicity. ..
  55. Transcriptional Silencing Near tRNA Genes
    DAVID ENGELKE; Fiscal Year: 2004
    ..The aims of this project are to investigate the mechanism of conditional tgm silencing in yeast. ..
  56. 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'
    John Atkins; Fiscal Year: 2004
    ..To keep monitoring newly reported sequences for potential new cases and to respond to suggestions of others who have encountered new cases. ..
  57. SMALL NOVEL RNA AGENTS FOR HCMV THERAPY
    Fenyong Liu; Fiscal Year: 2001
    ..These studies will reveal the mechanism of how EGSs achieve high targeting efficacy and sequence specificity and facilitate the development of these novel RNA agents for antiviral and anticancer applications. ..
  58. Upstream ORFs: A general strategy for virus attenuation
    Theo Dreher; Fiscal Year: 2006
    ..abstract_text> ..
  59. SIGNALING PATHWAYS & TRANSCRIPTIONAL REGULATION
    Ian Willis; Fiscal Year: 2003
    ..And prevent their energetically costly synthesis at inappropriate times. The long term goal of the proposed application is to elucidate the relationship between cell proliferation and transcription of the protein synthetic machinery. ..
  60. EFFECT OF DIABETES AND HYPERTENSION ON ISCHEMIC INJURY
    Stephen Schaffer; Fiscal Year: 2003
    ..Cell culture studies will be complimented by studies using an isolated heart model to test the hypothesis that hypertensive diabetic hearts will be more susceptible to an ischemic insole because of elevated levels of angiotensin. ..