ribosomes

Summary

Summary: A class of multicomponent structures found in all cells, in mitochondria, and chloroplasts. They have roles both in the genetic translation of transcripts and in the manufacture and secretion of the proteins. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

Top Publications

  1. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
  2. pmc Regulation of translation initiation in eukaryotes: mechanisms and biological targets
    Nahum Sonenberg
    Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, H3G 1Y6, Canada
    Cell 136:731-45. 2009
  3. ncbi The structure of the eukaryotic ribosome at 3.0 Å resolution
    Adam Ben-Shem
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch F 67400, France
    Science 334:1524-9. 2011
  4. pmc Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:789-802. 2011
  5. pmc The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    Gene Wei Li
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
    Nature 484:538-41. 2012
  6. ncbi An evolutionarily conserved mechanism for controlling the efficiency of protein translation
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Cell 141:344-54. 2010
  7. ncbi The economics of ribosome biosynthesis in yeast
    J R Warner
    Dept of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, Bronx, NY 10461, USA
    Trends Biochem Sci 24:437-40. 1999
  8. pmc Automated design of synthetic ribosome binding sites to control protein expression
    Howard M Salis
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Biotechnol 27:946-50. 2009
  9. ncbi Assembly of bacterial ribosomes
    Zahra Shajani
    Departments of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 80:501-26. 2011
  10. ncbi The post-transcriptional steps of eukaryotic ribosome biogenesis
    A K Henras
    Laboratoire de Biologie Moleculaire Eucaryote, CNRS, Universite de Toulouse, UPS, 118 route de Narbonne, 31062 Toulouse Cedex 09, France
    Cell Mol Life Sci 65:2334-59. 2008

Detail Information

Publications376 found, 100 shown here

  1. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
    ..Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible...
  2. pmc Regulation of translation initiation in eukaryotes: mechanisms and biological targets
    Nahum Sonenberg
    Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, H3G 1Y6, Canada
    Cell 136:731-45. 2009
    ....
  3. ncbi The structure of the eukaryotic ribosome at 3.0 Å resolution
    Adam Ben-Shem
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch F 67400, France
    Science 334:1524-9. 2011
    b>Ribosomes translate genetic information encoded by messenger RNA into proteins. Many aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are much larger and intricate than their bacterial counterparts...
  4. pmc Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:789-802. 2011
    ..We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein ..
  5. pmc The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    Gene Wei Li
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
    Nature 484:538-41. 2012
    Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding...
  6. ncbi An evolutionarily conserved mechanism for controlling the efficiency of protein translation
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Cell 141:344-54. 2010
    ..We suggest that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression...
  7. ncbi The economics of ribosome biosynthesis in yeast
    J R Warner
    Dept of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, Bronx, NY 10461, USA
    Trends Biochem Sci 24:437-40. 1999
    ..This is entrusted to a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, leading to major implications for the expression of other genes as well...
  8. pmc Automated design of synthetic ribosome binding sites to control protein expression
    Howard M Salis
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Biotechnol 27:946-50. 2009
    ..The proposed forward engineering approach should accelerate the construction and systematic optimization of large genetic systems...
  9. ncbi Assembly of bacterial ribosomes
    Zahra Shajani
    Departments of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 80:501-26. 2011
    The assembly of ribosomes from a discrete set of components is a key aspect of the highly coordinated process of ribosome biogenesis...
  10. ncbi The post-transcriptional steps of eukaryotic ribosome biogenesis
    A K Henras
    Laboratoire de Biologie Moleculaire Eucaryote, CNRS, Universite de Toulouse, UPS, 118 route de Narbonne, 31062 Toulouse Cedex 09, France
    Cell Mol Life Sci 65:2334-59. 2008
    One of the most important tasks of any cell is to synthesize ribosomes. In eukaryotes, this process occurs sequentially in the nucleolus, the nucleoplasm and the cytoplasm...
  11. pmc Specialized ribosomes: a new frontier in gene regulation and organismal biology
    Shifeng Xue
    Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
    Nat Rev Mol Cell Biol 13:355-69. 2012
    ..ribosomal RNA (rRNA) diversity and the activity of ribosome-associated factors may generate 'specialized ribosomes' that have a substantial impact on how the genomic template is translated into functional proteins...
  12. pmc Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
    Leonardo G Trabuco
    Beckman Institute, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Structure 16:673-83. 2008
    ..The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM...
  13. ncbi What recent ribosome structures have revealed about the mechanism of translation
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Nature 461:1234-42. 2009
    ..In this review, we discuss how the interaction between structural and functional studies over the last decade has led to a deeper understanding of the complex mechanisms underlying translation...
  14. ncbi Crystal structure of the eukaryotic ribosome
    Adam Ben-Shem
    IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F 67400, France
    Science 330:1203-9. 2010
    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes...
  15. ncbi Translational control in stress and apoptosis
    Martin Holcik
    Apoptosis Research Center, Room R3116, Children s Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
    Nat Rev Mol Cell Biol 6:318-27. 2005
    ....
  16. pmc Ribosomopathies: human disorders of ribosome dysfunction
    Anupama Narla
    Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Blood 115:3196-205. 2010
    ..Elucidation of the mechanisms whereby selective abnormalities in ribosome biogenesis cause specific clinical syndromes will hopefully lead to novel therapeutic strategies for these diseases...
  17. ncbi Driving ribosome assembly
    Dieter Kressler
    Biochemie Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
    Biochim Biophys Acta 1803:673-83. 2010
    ..This review summarizes our current knowledge on eukaryotic ribosome assembly, with particular focus on the molecular role of the involved energy-consuming enzymes...
  18. ncbi A role for codon order in translation dynamics
    Gina Cannarozzi
    Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
    Cell 141:355-67. 2010
    ..They also establish that the dynamics of translation leave a significant signature at the level of the genome...
  19. ncbi Analysis of the aphthovirus 2A/2B polyprotein 'cleavage' mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal 'skip'
    M L Donnelly
    Centre for Biomolecular Sciences, School of Biology, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
    J Gen Virol 82:1013-25. 2001
    ..This process produces a ribosomal 'skip' from one codon to the next without the formation of a peptide bond...
  20. pmc Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells
    Krishna M Vattem
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Proc Natl Acad Sci U S A 101:11269-74. 2004
    ..When eIF2-GTP is abundant in nonstressed cells, ribosomes scanning downstream of uORF1 reinitiate at the next coding region, uORF2, an inhibitory element that blocks ATF4 ..
  21. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
    ....
  22. ncbi Systematic identification of pathways that couple cell growth and division in yeast
    Paul Jorgensen
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Science 297:395-400. 2002
    ..Cell growth and division appear to be coupled by multiple conserved mechanisms...
  23. pmc Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells
    Somenath Bakshi
    Department of Chemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    Mol Microbiol 85:21-38. 2012
    Quantitative spatial distributions of ribosomes (S2-YFP) and RNA polymerase (RNAP; β'-yGFP) in live Escherichia coli are measured by superresolution fluorescence microscopy...
  24. pmc The structure of the ribosome with elongation factor G trapped in the posttranslocational state
    Yong Gui Gao
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
    Science 326:694-9. 2009
    ..The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure...
  25. pmc Wobble base-pairing slows in vivo translation elongation in metazoans
    Michael Stadler
    Department of Genetics, Stanford University, Stanford, California 94305 5324, USA
    RNA 17:2063-73. 2011
    ..These data support a model in which ribosomal translocation is slowed at wobble codon positions...
  26. ncbi MYC as a regulator of ribosome biogenesis and protein synthesis
    Jan van Riggelen
    Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Rev Cancer 10:301-9. 2010
    ..MYC coordinates protein synthesis through the transcriptional control of RNA and protein components of ribosomes, and of gene products required for the processing of ribosomal RNA, the nuclear export of ribosomal subunits and ..
  27. ncbi One core, two shells: bacterial and eukaryotic ribosomes
    Sergey Melnikov
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France
    Nat Struct Mol Biol 19:560-7. 2012
    b>Ribosomes are universally conserved enzymes that carry out protein biosynthesis...
  28. pmc A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease
    Sander Granneman
    Wellcome Trust Centre for Cell Biology and Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, Scotland
    EMBO J 30:4006-19. 2011
    ..8S 3'- and 25S 5'-regions, which are base paired in mature ribosomes, and in the ITS2 spacer that separates these rRNAs...
  29. pmc Following translation by single ribosomes one codon at a time
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 452:598-603. 2008
    We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation--and-pause cycles...
  30. ncbi Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
    Gong Zhang
    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nat Struct Mol Biol 16:274-80. 2009
    ..We propose that local discontinuous translation temporally separates the translation of segments of the peptide chain and actively coordinates their co-translational folding...
  31. ncbi MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome
    Yolanda Camara
    Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
    Cell Metab 13:527-39. 2011
    ..Loss of MTERF4 leads to defective ribosomal assembly and a drastic reduction in translation. Our results thus show that MTERF4 is an important regulator of translation in mammalian mitochondria...
  32. ncbi Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning
    Nadya Kondrashov
    Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, 94158, USA
    Cell 145:383-97. 2011
    ..Collectively, these findings suggest that RP activity may be highly regulated to impart a new layer of specificity in the control of gene expression and mammalian development...
  33. pmc Comprehensive molecular structure of the eukaryotic ribosome
    Derek J Taylor
    Wadsworth Center, Empire State Plaza, Albany, NY 12201 0509, USA
    Structure 17:1591-604. 2009
    ..Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in ..
  34. pmc Ribosome deficiency protects against ER stress in Saccharomyces cerevisiae
    Kristan K Steffen
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Genetics 191:107-18. 2012
    ....
  35. pmc Cotranslational response to proteotoxic stress by elongation pausing of ribosomes
    Botao Liu
    Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, NY 14853, USA
    Mol Cell 49:453-63. 2013
    ..Here we report that intracellular proteotoxic stress reduces global protein synthesis by halting ribosomes on transcripts during elongation...
  36. 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
    ....
  37. ncbi Crystal structure of the 80S yeast ribosome
    Lasse Jenner
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F 67400, France
    Curr Opin Struct Biol 22:759-67. 2012
    The first X-ray structure of the eukaryotic ribosome at 3.0Å resolution was determined using ribosomes isolated and crystallized from the yeast Saccharomyces cerevisiae (Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, ..
  38. ncbi Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease
    Claudine Kraft
    Institute of Biochemistry, HPM, ETH Honggerberg, 8093 Zurich, Switzerland
    Nat Cell Biol 10:602-10. 2008
    ..Here we show that mature ribosomes are rapidly degraded by autophagy upon nutrient starvation in Saccharomyces cerevisiae...
  39. ncbi Molecular mechanisms of translational control
    Fátima Gebauer
    Centre de Regulacio Genomica, Passeig Maritim 37 49, 08003 Barcelona, Spain
    Nat Rev Mol Cell Biol 5:827-35. 2004
    ..Instead of providing a comprehensive account of the examples that are known at present, we discuss instructive cases that serve as paradigms for different modes of translational control...
  40. pmc How common are extraribosomal functions of ribosomal proteins?
    Jonathan R Warner
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Mol Cell 34:3-11. 2009
    ..Is this due to a lack of imaginative evolution by cells and viruses, or to a lack of imaginative experiments by molecular biologists?..
  41. pmc A ribosome-associating factor chaperones tail-anchored membrane proteins
    Malaiyalam Mariappan
    Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 466:1120-4. 2010
    ..This Bat3 complex is recruited to ribosomes synthesizing membrane proteins, interacts with the TMDs of newly released TA proteins, and transfers them to ..
  42. 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)...
  43. pmc Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein
    Ying Fang
    Departments of Veterinary and Biomedical Science and Biology Microbiology, South Dakota State University, Brookings, SD 57007, USA
    Proc Natl Acad Sci U S A 109:E2920-8. 2012
    ..Our findings demonstrate that -2 PRF is a functional gene-expression mechanism in eukaryotes and add another layer to the complexity of arterivirus genome expression...
  44. pmc Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress
    Maxim V Gerashchenko
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:17394-9. 2012
    ..These data define the landscape of genome-wide regulation of translation in response to hydrogen peroxide and suggest that potentiation (coregulation of the transcript level and translation) is a feature of oxidative stress...
  45. pmc Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution
    Jean Paul Armache
    Gene Center, Department of Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Proc Natl Acad Sci U S A 107:19748-53. 2010
    ..the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ..
  46. 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
    ..The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation...
  47. 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
    ..The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs...
  48. ncbi Growth control and ribosome biogenesis
    Harri Lempiäinen
    Department of Molecular Biology and NCCR Program Frontiers in Genetics, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4, Switzerland
    Curr Opin Cell Biol 21:855-63. 2009
    b>Ribosomes provide the basis for protein production and this drives cell growth...
  49. pmc Cryo-EM structure of the ribosome-SecYE complex in the membrane environment
    Jens Frauenfeld
    Gene Center, Department for Biochemistry, University of Munich, Munich, Germany
    Nat Struct Mol Biol 18:614-21. 2011
    ..On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane...
  50. pmc Putatively noncoding transcripts show extensive association with ribosomes
    Benjamin A Wilson
    Department of Ecology and Evolutionary Biology, University of Arizona, USA
    Genome Biol Evol 3:1245-52. 2011
    ..Here we analyze Saccharomyces cerevisiae data on noncoding transcripts found in association with ribosomes. We find many such transcripts...
  51. pmc Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome
    Jean Paul Armache
    Gene Center, Department of Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Proc Natl Acad Sci U S A 107:19754-9. 2010
    Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in ..
  52. pmc The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
    Science 326:688-94. 2009
    ..A series of conformational changes in EF-Tu and aminoacyl-tRNA suggests a communication pathway between the decoding center and the guanosine triphosphatase center of EF-Tu...
  53. pmc Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    Sergey Proshkin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 328:504-8. 2010
    ..Such a cooperative mechanism ensures that the transcriptional yield is always adjusted to translational needs at different genes and under various growth conditions...
  54. pmc Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation
    Meenakshi K Doma
    Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
    Nature 440:561-4. 2006
    ..No-go decay provides a mechanism for clearing the cell of stalled translation elongation complexes, which could occur as a result of damaged mRNAs or ribosomes, or as a mechanism of post-transcriptional control.
  55. ncbi eIF3: a versatile scaffold for translation initiation complexes
    Alan G Hinnebusch
    Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Trends Biochem Sci 31:553-62. 2006
    ..This location of eIF3 seems ideally suited for its other proposed regulatory functions, including reinitiating translation on polycistronic mRNAs and acting as a receptor for protein kinases that control protein synthesis...
  56. pmc Ribosomal protein L11 negatively regulates oncoprotein MDM2 and mediates a p53-dependent ribosomal-stress checkpoint pathway
    Yanping Zhang
    Department of Molecular and Cellular Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Mol Cell Biol 23:8902-12. 2003
    ..We suggest that L11 functions as a negative regulator of HDM2 and that there might exist in vivo an L11-HDM2-p53 pathway for monitoring ribosomal integrity...
  57. pmc Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo
    Eugene Oh
    Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:1295-308. 2011
    As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors...
  58. pmc Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast
    Christopher J Shoemaker
    Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 108:E1392-8. 2011
    ..These results establish a model in which eukaryotic termination and recycling are not clearly demarcated events, as they are in bacteria, but coupled stages of the same release-factor mediated process...
  59. pmc Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins
    Yun Wah Lam
    Division of Gene Regulation and Expression, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Curr Biol 17:749-60. 2007
    ....
  60. ncbi The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    N Ban
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    Science 289:905-20. 2000
    ..Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior...
  61. pmc Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome
    Thomas Becker
    Gene Center Munich and Center for Integrated Protein Science, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 326:1369-73. 2009
    ..This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation...
  62. ncbi Ribosome biogenesis and cell growth: mTOR coordinates transcription by all three classes of nuclear RNA polymerases
    C Mayer
    Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
    Oncogene 25:6384-91. 2006
    ..Expression of the genes encoding the numerous constituents of ribosomes requires transcription by all three classes of nuclear RNA polymerases...
  63. ncbi Ribosome engineering and secondary metabolite production
    Kozo Ochi
    National Food Research Institute Ibaraki 305 8642, Japan
    Adv Appl Microbiol 56:155-84. 2004
  64. ncbi Speeding with control: codon usage, tRNAs, and ribosomes
    Eva Maria Novoa
    Institute for Research in Biomedicine IRB, c Baldiri Reixac 15 21 08028, Barcelona, Catalonia, Spain
    Trends Genet 28:574-81. 2012
    ..Here, we discuss the importance of codon-anticodon interactions in translation regulation and highlight the contribution of non-random codon distributions and post-transcriptional base modifications to this regulation...
  65. ncbi ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli
    Yuhei Chadani
    Graduate School of Natural Science and Technology, Okayama University, Okayama 700 8530, Japan
    Mol Microbiol 86:37-50. 2012
    The ribosomes stalled at the end of non-stop mRNAs must be rescued for productive cycles of cellular protein synthesis...
  66. pmc Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling
    David W Reid
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Biol Chem 287:5518-27. 2012
    ..and topogenic signal-encoding proteins display similar ribosome loading densities, suggesting that ER-associated ribosomes serve a global role in mRNA translation...
  67. ncbi Ribosome biogenesis surveillance: probing the ribosomal protein-Mdm2-p53 pathway
    C Deisenroth
    Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    Oncogene 29:4253-60. 2010
    ..Growth is driven by new protein synthesis, a process that requires robust manufacture of ribosomes in the nucleolus...
  68. ncbi The multifunctional nucleolus
    Francois Michel Boisvert
    Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, UK
    Nat Rev Mol Cell Biol 8:574-85. 2007
    ....
  69. ncbi rRNA modifications and ribosome function
    Wayne A Decatur
    Trends Biochem Sci 27:344-51. 2002
    The development of three-dimensional maps of the modified nucleotides in the ribosomes of Escherichia coli and yeast has revealed that most (approximately 95% in E. coli and 60% in yeast) occur in functionally important regions...
  70. ncbi Translational pausing ensures membrane targeting and cytoplasmic splicing of XBP1u mRNA
    Kota Yanagitani
    Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916 5, Takayama, Ikoma, Nara 630 0192, Japan
    Science 331:586-9. 2011
    ..Thus, translational pausing may be used for unexpectedly diverse cellular processes in mammalian cells...
  71. pmc A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites
    Cynthia M Sharma
    RNA Biology Group, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
    Genes Dev 21:2804-17. 2007
    ..Taken together, our study suggests highly conserved regions in sRNAs and mRNA regions distant from Shine-Dalgarno sequences as important elements for the identification of sRNA targets...
  72. ncbi Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation
    A A Komar
    Centre de Genetique Moleculaire, CNRS, Gif sur Yvette, France
    FEBS Lett 462:387-91. 1999
    ..coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein-folding pathway, leading to increased levels of protein misfolding...
  73. pmc Powering through ribosome assembly
    Bethany S Strunk
    Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    RNA 15:2083-104. 2009
    ..Finally, we use literature data to suggest testable models for how these enzymes could be used as targets for regulation of ribosome assembly...
  74. pmc Ribosome biogenesis and the translation process in Escherichia coli
    Magdalena Kaczanowska
    Department of Genetics, Microbiology, and Toxicology, Stockholm University, S 10691 Stockholm, Sweden
    Microbiol Mol Biol Rev 71:477-94. 2007
    ..When finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked...
  75. ncbi mRNA helicase activity of the ribosome
    Seyedtaghi Takyar
    Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 120:49-58. 2005
    ..Until now, no helicase activity has been identified which could account for the ability of ribosomes to translate through downstream mRNA secondary structure...
  76. pmc Maturation of eukaryotic ribosomes: acquisition of functionality
    Vikram Govind Panse
    Institute of Biochemistry IBC, ETH Zurich, CH 8093, Zurich, Switzerland
    Trends Biochem Sci 35:260-6. 2010
    In eukaryotic cells, ribosomes are pre-assembled in the nucleus and exported to the cytoplasm where they undergo final maturation...
  77. ncbi Regulated translation initiation controls stress-induced gene expression in mammalian cells
    H P Harding
    Skirball Institute of Biomolecular Medicine The Department of Medicine, Kaplan Cancer Center New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 6:1099-108. 2000
    ..Mammalian cells thus utilize an ancient pathway to regulate gene expression in response to diverse stress signals...
  78. pmc Structure and function of HCV IRES domains
    Peter J Lukavsky
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge CB2 0QH, UK
    Virus Res 139:166-71. 2009
    ..structural features of IRES domains and how these RNA motifs function as RNA-based initiation factors to form 48S initiation complexes and 80S ribosomes with only a subset of canonical, protein-based eukaryotic initiation factors.
  79. pmc Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning
    Katherine E Berry
    Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
    Structure 19:1456-66. 2011
    ....
  80. pmc The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae
    Dominique Chu
    School of Computing, University of Kent, CT2 7NF, UK
    Nucleic Acids Res 39:6705-14. 2011
    ..translation in Saccharomyces cerevisiae for the investigation of two particular translational resources, namely ribosomes and aminoacylated tRNAs...
  81. ncbi Introns within ribosomal protein genes regulate the production and function of yeast ribosomes
    Julie Parenteau
    Laboratoire de génomique fonctionnelle de l Université de Sherbrooke, Departement de Microbiologie et d Infectiologie, Faculte de Medecine et des Sciences de la Sante, Universite de Sherbrooke, Quebec, Canada
    Cell 147:320-31. 2011
    ..Together, our results indicate that splicing in yeast RP genes mediates intergene regulation and implicate the expression ratio of duplicated RP genes in modulating ribosome function...
  82. pmc Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes
    Vera P Pisareva
    Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
    EMBO J 30:1804-17. 2011
    ..ABCE1/Pelota/Hbs1 also dissociated vacant 80S ribosomes, which stimulated 48S complex formation, suggesting that Pelota/Hbs1 have an additional role outside of NGD.
  83. pmc FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism
    Jennifer C Darnell
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, NY 10065, USA
    Cell 146:247-61. 2011
    ..We developed a brain polyribosome-programmed translation system, revealing that FMRP reversibly stalls ribosomes specifically on its target mRNAs...
  84. pmc Structural insight into nascent polypeptide chain-mediated translational stalling
    Birgit Seidelt
    Gene Center and Center for Integrated Protein Science Munich CIPSM, Department for Chemistry and Biochemistry, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 326:1412-5. 2009
    ..We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel...
  85. ncbi 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors
    Paola Grandi
    Cellzome AG, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Mol Cell 10:105-15. 2002
    ..Mutations in components of the 90S pre-ribosomes impaired 40S subunit assembly and export...
  86. pmc Divergent stalling sequences sense and control cellular physiology
    Koreaki Ito
    Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita ku, Kyoto 603 8555, Japan
    Biochem Biophys Res Commun 393:1-5. 2010
    ....
  87. pmc How the sequence of a gene can tune its translation
    Kurt Fredrick
    Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
    Cell 141:227-9. 2010
    ..Two new studies (Cannarrozzi et al., 2010; Tuller et al., 2010) now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning translation to increase the efficiency of protein synthesis...
  88. pmc Differential contribution of the m7G-cap to the 5' end-dependent translation initiation of mammalian mRNAs
    Dmitri E Andreev
    Belozersky Institute of Physico Chemical Biology, Moscow State University, Moscow 119992, Russia
    Nucleic Acids Res 37:6135-47. 2009
    ..Thus, it is not mandatory to invoke the IRES hypothesis, at least for some mRNAs, to explain their preferential translation when eIF4E is partially inactivated...
  89. ncbi Release of eIF6 (p27BBP) from the 60S subunit allows 80S ribosome assembly
    Marcello Ceci
    Molecular Histology Unit, DiBiT HSR, 20132 Milano, Italy
    Nature 426:579-84. 2003
    The assembly of 80S ribosomes requires joining of the 40S and 60S subunits, which is triggered by the formation of an initiation complex on the 40S subunit...
  90. ncbi Real-time tRNA transit on single translating ribosomes at codon resolution
    Sotaro Uemura
    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305 5126, USA
    Nature 464:1012-7. 2010
    ..codon is monitored by stable binding of transfer RNAs (tRNAs)-labelled with distinct fluorophores-to translating ribosomes, which allows direct detection of the identity of tRNA molecules bound to the ribosome and therefore the ..
  91. pmc Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale
    Odile Lecompte
    Laboratoire de Biologie et Genomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS, INSERM, ULP, BP163, 67404 Illkirch Cedex, France
    Nucleic Acids Res 30:5382-90. 2002
    ..This first documented case of reductive evolution at the domain scale provides a new framework for discussing the shape of the universal tree of life and the selective forces directing the evolution of prokaryotes...
  92. pmc Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action
    Jack A Dunkle
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:17152-7. 2010
    Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics...
  93. pmc La autoantigen is necessary for optimal function of the poliovirus and hepatitis C virus internal ribosome entry site in vivo and in vitro
    Mauro Costa-Mattioli
    Department of Biochemistry and McGill Cancer Center, McGill University, McIntyre Medical Building, Montreal, Quebec, Canada H3G 1Y6
    Mol Cell Biol 24:6861-70. 2004
    Translation of poliovirus and hepatitis C virus (HCV) RNAs is initiated by recruitment of 40S ribosomes to an internal ribosome entry site (IRES) in the mRNA 5' untranslated region...
  94. pmc Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites
    Sylvain de Breyne
    Department of Microbiology and Immunology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
    Proc Natl Acad Sci U S A 106:9197-202. 2009
    ..These data suggest that fundamental aspects of the mechanisms of initiation on these unrelated classes of IRESs are similar...
  95. pmc Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family
    Daniel H Haft
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Biol 8:70. 2010
    ..TOMM peptides are small and highly variable, frequently missed by gene-finders and occasionally situated far from the thiazole/oxazole forming genes. Thus, locating a substrate for a particular TOMM pathway can be a challenging endeavor...
  96. pmc Follow the leader: the use of leader peptides to guide natural product biosynthesis
    Trent J Oman
    Department of Chemistry, Howard Hughes Medical Institute, and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Nat Chem Biol 6:9-18. 2010
    ....
  97. pmc RNA tertiary interactions in the large ribosomal subunit: the A-minor motif
    P Nissen
    Department of Molecular Biophysics and Biochemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA
    Proc Natl Acad Sci U S A 98:4899-903. 2001
    ..It may prove to be the universally most important long-range interaction in large RNA structures...
  98. pmc Ribosomal protein L23 activates p53 by inhibiting MDM2 function in response to ribosomal perturbation but not to translation inhibition
    Mu Shui Dai
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97201, USA
    Mol Cell Biol 24:7654-68. 2004
    ..These results reveal that L23 is another regulator of the p53-MDM2 feedback regulation...
  99. ncbi Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy
    Niels Fischer
    3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Nature 466:329-33. 2010
    ..The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement...
  100. pmc Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly
    Tadepalli Adilakshmi
    T C Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 2685, USA
    Nature 455:1268-72. 2008
    Rapidly growing cells produce thousands of new ribosomes each minute, in a tightly regulated process that is essential to cell growth...
  101. ncbi The weird and wonderful world of bacterial ribosome regulation
    Daniel N Wilson
    Gene Center and Department of Chemistry and Biochemistry, University of Munich, Munich, Germany
    Crit Rev Biochem Mol Biol 42:187-219. 2007
    ....

Research Grants70

  1. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2012
    ..In experimental animals, these mycotoxins and other natural toxins that bind with high affinity to eukaryotic ribosomes (eg. ricin, Shiga toxin, anisomycin) induce proinflammatory gene expression and apoptosis in lymphoid tissues...
  2. MEMBRANES OF THE DENTAL PATHOGEN STREPTOCOCCUS MUTANS
    L Jeannine Brady; Fiscal Year: 2013
    ..2) to establish the role of YidC2 in co-translational translocation and its interaction with streptococcal ribosomes using chemical cross-linking and immunoprecipitation, and 3) to dissect the composition and interactions among ..
  3. Structure and Function of the Hepatitis C Virus Genome
    Peter Sarnow; Fiscal Year: 2013
    ..It was discovered that HCV binds ribosomes by a novel, unprecedented mechanism of internal ribosome binding, and that a key defense protein against viruses,..
  4. Characterization of an essential mitochondrial rRNA methyltransferase
    Kip E Guja; Fiscal Year: 2013
    ..two adjacent adenine residues in a conserved stem-loop in the small subunit of the bacterial and eukaryotic ribosomes, respectively...
  5. Role of Coxiella burnetii group I introns in growth modulation
    Michael F Minnick; Fiscal Year: 2010
    ..Aim 1 will examine ribosome inhibition by ribozymes. Preliminary data show that both ribozymes associate with ribosomes of Coxiella or E. coli. Data also show that ribozymes retard growth of both bacteria...
  6. HORMONAL REGULATION OF MESSENGER RNA STABILITY
    Daniel R Schoenberg; Fiscal Year: 2013
    ..of a subset of the transcriptome is catalyzed by endonuclease cleavage while mRNAs are engaged by translating ribosomes. The prototypical mRNA endonuclease is PMR1, an en- zyme that was originally identified as an estrogen-induced ..
  7. IRES-mediated translation initiation on viral mRNAs
    CHRISTOPHER ULRICH TRISTRAM HELLEN; Fiscal Year: 2013
    ..and complexity of IRESs varies, but they all coordinate the activities of protein factors in order to recruit ribosomes to translate viral proteins and are consequently essential for virus viability...
  8. Mitochondrial Inborn Errors in Metabolism
    Douglas C Wallace; Fiscal Year: 2013
    ..The former mRNAs will be translated on cytosolic ribosomes and the protein imported into the mitochondrion while the latter will carry RNA import signals to induce the ..
  9. Model systems for hematologic disorders caused by ribosomal protein deficiency
    George Thomas; Fiscal Year: 2010
    ..mass to enter the cell cycle, and (ii) it ensures that each daughter cell obtains the appropriate number of ribosomes. Given that a change in the ratio of ribosomes to mRNA would eventually modify the pattern of translation and ..
  10. Role of the ribosomal stalk in the activity of Shiga toxins
    Nilgun E Tumer; Fiscal Year: 2013
    ..We propose to examine the interaction of Stx1 and Stx2 with ribosomes from yeast and mammalian cells to test the hypothesis that they differ in their requirements for the ribosomal ..
  11. The mechanism of mRNA recruitment to the human ribosome.
    Christopher S Fraser; Fiscal Year: 2013
    ..III. Determine how human ribosomes scan along the 5" untranslated region (5"UTR) to locate the AUG codon...
  12. Regulation and Function of Germline RNP Granules
    JENNIFER SCHISA; Fiscal Year: 2010
    ..includes an ultrastructural characterization of germline RNPs to determine if nuclear pores, mitochondria, and ribosomes are differentially localized in germlines when ovulation is arrested or stress is present...
  13. Facilitating large scale biomass generation: acquisition of an automated 100 L fe
    Roger D Kornberg; Fiscal Year: 2010
    ..Large amounts of ribosomes, accessory proteins, and tRNAs are required...
  14. Processing and consequences of DNA-protein crosslinks in E. coli
    Kenneth N Kreuzer; Fiscal Year: 2012
    ..proposed that the DNA-protein crosslinks block transcription, which leads to blockage of the coupled translating ribosomes, to trigger the tmRNA system into action...
  15. Functions of 5'NCRs of picornavirus and cellular mRNAs
    Bert L Semler; Fiscal Year: 2013
    ..approaches to determine if this cleavage is responsible for clearing poliovirus genomic RNAs of translating ribosomes prior to the onset of viral RNA synthesis, providing a mechanistic switch for these two competing functions ..
  16. Membrane Protein Trafficking in Photoreceptors
    Wolfgang Baehr; Fiscal Year: 2013
    ..Integral membrane proteins are synthesized by ER-associated ribosomes and exported to the Golgi apparatus...
  17. Single Molecule Dynamics of mRNA Translation
    Yale E Goldman; Fiscal Year: 2013
    ..Our overall goal is to address this lack by quantifying the modulation of the rate of translation by E. coli ribosomes of specific mRNA and nascent peptide sequences, and to elucidate the mechanisms of such modulation...
  18. Control of cap-independent translation by a viral 3'UTR
    WYATT ALLEN MILLER; Fiscal Year: 2013
    ..functions in mammalian cells and we will use human cells and extracts to study how it uses eIF4E to usurp the ribosomes. Over-active eIF4E causes tumors and restriction of its function inhibits many types of cancers...
  19. A cell-based HTS for delayed death inhibitors of the malarial parasite plastid
    DAVID FIDOCK; Fiscal Year: 2009
    ..Detailed studies with antibiotics that target apicoplast ribosomes (such as azithromycin) reveal that apicoplast inhibitors manifest a unique delayed death phenotype, whereby only ..
  20. Structural and Dynamical Response of Escherichia coli to Osmotic Stress
    James C Weisshaar; Fiscal Year: 2010
    ..In this project we study protein transport (diffusion) and the organization of proteins, DNA, and ribosomes within the cytoplasm of live cells using fluorescence microscopy...
  21. Molecular Phenotyping of NOD Mice
    Ivan C Gerling; Fiscal Year: 2010
    ..increases in cell turn- over) and more universal defects present in both islets and immune cells (alterations in ribosomes and mitochondria)...
  22. Isolation of ribonucleic acids that are attached to the neuronal membrane
    Terunaga Nakagawa; Fiscal Year: 2013
    ..The proteins in the ribosomes have rather accessory and regulatory roles that are acquired later during evolution...
  23. In vivo observations of transcription at single-nucleotide resolution
    MATTHEW HERBERT LARSON; Fiscal Year: 2013
    ..it remains to be established whether these pauses persist unchanged in the cellular environment, where both ribosomes and transcription factors may alter transcription dynamics...
  24. Nucleic Acid Enzymes and Nucleic Acids Studied at the Molecular Level
    Steven M Block; Fiscal Year: 2013
    ..carried out by a handful of essential biomolecules that include polymerases, helicases, isomerases, and ribosomes. Together, these enzymes constitute a core group of sophisticated, bio- molecular machines...
  25. Visualizing Genetic Activity in Normal &Mutant Yeast
    Ann L Beyer; Fiscal Year: 2013
    ..This rRNA becomes the major structural and functional component of ribosomes and its rate of synthesis determines the rate of ribosome biogenesis, which in turn is directly correlated with ..
  26. INTERACTIONS BETWEEN AGROBACTERIUM AND HOST PLANTS
    Stephen C Winans; Fiscal Year: 2010
    ..that TraR and CepR require AHL for correct folding, and must bind this pheromone during their own synthesis on ribosomes. We will also study how the activating region or regions of TraR interact with RNA polymerase...
  27. Ty3 viruslike particle morphogenesis and host interactions
    Suzanne Sandmeyer; Fiscal Year: 2013
    ..Second, RNA-seq will be performed at the UCI Genomics High- Throughput Facility to map the association of ribosomes and Gag3 and PB proteins with Ty3 RNA...
  28. The Function of rpL5 and rpL11 in induction of p53
    George Thomas; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): A proliferating cell expends most of its energy in the biogenesis of nascent ribosomes. The increased number of ribosomes provides the translational capacity required for the cell to synthesize the ..
  29. BIOSYNTHESIS OF THE CYCLIC PEPTIDE TOXINS OF AMANITA MUSHROOMS
    Jonathan Walton; Fiscal Year: 2013
    ..For example, they are the smallest known peptides synthesized on ribosomes, and some of them already are known to have strong and unique biological targets...
  30. Translational Control of Oxidative Stress in Myocardial Infarction
    Qin M Chen; Fiscal Year: 2010
    ..A group of IRES Trans-Acting Factors (ITAFs) appears to be critical in recruiting the ribosomes to initiate the translation of these genes...
  31. Structural Aspects of Protein Synthesis in the Mammalian Mitochondria
    Rajendra K Agrawal; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Ribosomes are large ribonucleoprotein complexes, which interact with a number of protein factors and RNA molecules to carry out the essential process of protein biosynthesis, or translation, in all ..
  32. Ribosome Profiling in Plasmodium falciparum
    Marilyn Parsons; Fiscal Year: 2013
    ..erythrocytic stages by coupling the ability to isolate the speciic "footprints" of mRNAs that are occupied by ribosomes (an indicator of translation) with the depth and breadth of next generation sequencing...
  33. The Role of Ribosomal RNA Modifications
    Christine S Chow; Fiscal Year: 2012
    ..fluorescence spectroscopy), 2) use chemical probing and biological assays on full-length ribosomal RNAs and ribosomes to reveal whether structural changes observed in model systems are relevant in natural systems, and 3) identify ..
  34. New Gene Discoveries and Biology of Ribosomes in Diamond-Blackfan Anemia
    HANNA TERESA GAZDA; Fiscal Year: 2013
    ..Specific Aim 2. Determine the role of DBA genes in pre-RNA maturation. Specific Aim 3. Identify modifier genes in DBA by performing a genome-wide association study. ..
  35. New gene discoveries and biology of ribosomes in Diamond-Blackfan anemia.
    HANNA TERESA GAZDA; Fiscal Year: 2013
    ..Specific Aim 2. Determine the role of DBA genes in pre-RNA maturation. Specific Aim 3. Identify modifier genes in DBA by performing a genome-wide association study. ..
  36. REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNA
    Geoffrey M Kapler; Fiscal Year: 2010
    ..We hypothesize that 26T RNA is processed from cytoplasmic ribosomes and functions as a physiological link between DNA replication and cellular metabolism...
  37. CYTOPLASMIC LIPID BODIES OF INFLAMMATORY CELLS
    Peter F Weller; Fiscal Year: 2013
    ..proteomic and ultrastructural studies, leukocyte lipid bodies are complex organelles with internal membranes and ribosomes whose proteome includes proteins involved in protein synthesis...
  38. Mechanism and targets of non-stop decay in eukaryotic translation
    KRISTIN SMITH-KOUTMOU; Fiscal Year: 2013
    ..NSD targets transcripts lacking stop codons, which not only generate aberrant proteins, but also stall ribosomes, leading to an overall decrease in translation efficiency...
  39. Optimization of Small-Molecule Inhibitors of Shiga and Ricin Toxins
    Yuan Ping Pang; Fiscal Year: 2012
    ..knowledge useful for identification and optimization of other small-molecule inhibitors of toxins that target ribosomes;(3) a proof-of- concept for use of small-molecule inhibitors as adjuncts to immunization to explore the synergy ..
  40. ASSEMBLY OF MEMBRANES IN HEART AND YEAST MITOCHONDRIA
    ALEXANDER A TZAGOLOFF; Fiscal Year: 2013
    ..to study the mechanisms by which the H+ translocating ATPase (F1-F0 ATPase), the bc1 complex and mitochondrial ribosomes are assembled. In the coming period we intend to continue three areas of studies...
  41. What makes ricin toxic
    Nilgun E Tumer; Fiscal Year: 2013
    ..The toxicity of ricin is thought to be due to irreversibe inactivation of ribosomes and subsequent translational arrest...
  42. A New E3 Ligase Implicated in Protein Quality Control and Neurodegeneration
    Claudio A P Joazeiro; Fiscal Year: 2013
    ..are that (a) Listerin acts in protein quality control by ubiquitinating non-stop polypeptides stalled in ribosomes, and (b) defective Listerin-mediated degradation leads to the formation of protein aggregates and inclusions, ..
  43. RNA trafficking in mitochondria
    Michael A Teitell; Fiscal Year: 2013
    ..The translation of this limited number of mitochondrial coded proteins requires mitochondrial ribosomes, translation factors, and transfer RNAs...
  44. High Throughput Screening for Foot and Mouth Disease Virus Antivirals
    John F Atkins; Fiscal Year: 2013
    ..b>Ribosomes translate 2A conventionally but then stop, releasing the 2A product, before immediately restarting to make 2B...
  45. Nucleophosmin and ribosomal dysfunction in hematologic diseases
    Pier Paolo Pandolfi; Fiscal Year: 2010
    ..preliminary data indicate that primary cells from these mice that are haploinsufficient for Npm1 harbor aberrant ribosomes, and such qualitative differences in ribosome composition can lead to significantly different translational ..
  46. Novel technology for analysis of cardiac &BMP-specific gene expression profiling
    TODD ANDREW TOWNSEND; Fiscal Year: 2013
    ..Thus, only defined cell lineages will have both the BRLP-tagged ribosomes and the BirA enzyme will have ribosomes that are tagged with biotin...
  47. Specialized ribosomes in control of gene expression and embryonic development
    Maria Barna; Fiscal Year: 2011
    ..b>Ribosomes are molecular machines that carry out the daunting task of translating all the mRNAs expressed by the genome ..
  48. The mechanisms of eukaryotic translation termination and ribosomal recycling
    Tatyana V Pestova; Fiscal Year: 2013
    ..g. stable secondary structure. It is initiated by endonucleolytic cleavage in the vicinity of stalled ribosomes, which s stimulated by eRF1 and eRF3 paralogues Pelota and Hbs1 that together with ABCE1 can then dissociate ECs ..
  49. Ribosome profiling of Trypanosoma brucei
    Marilyn Parsons; Fiscal Year: 2012
    ..technology that couples the ability to isolate the specific "footprints" of mRNAs that are occupied by ribosomes (an indicator of translation) with the depth and breadth of next generation sequencing...
  50. Pyrazinamide and Trans-Translation in Mycobacterium tuberculosis
    Ying Zhang; Fiscal Year: 2013
    ..in both translation and ribosome rescuing process called trans-translation involved in management of stalled ribosomes and damaged proteins and RNA during stress...
  51. Role of rRNA Modifications in Dyskeratosis Congenita and Translation Control
    Davide Ruggero; Fiscal Year: 2009
    ..Finally, in Aim 3 we will determine the molecular step(s) in which DKC1m ribosomes fail to initiate protein synthesis utilizing an in vitro reconstituted system. Lay abstract...
  52. Host-pathogen interactions in hepatitis C virus replication
    SHELTON STEWART BRADRICK; Fiscal Year: 2013
    ..internal ribosome entry site (IRES) located within the viral 5'untranslated region (UTR) recruits cellular ribosomes to mediate synthesis of viral proteins required for replication...
  53. ASSEMBLY OF MEMBRANES IN HEART AND YEAST MITOCHONDRIA
    Alexander Tzagoloff; Fiscal Year: 2009
    ..of complex membrane enzymes such as the H+-translocating ATPase, the bc1 complex and more recently mitochondrial ribosomes. During the last period substantial progress was made on several fronts including the pathway of ATPase ..
  54. RNA Nanotechnology in Cancer Therapy
    JOHN JOSEPH ROSSI; Fiscal Year: 2013
    ..This application proposes to fabricate RNA nanoparticles to incorporate therapeutic SiRNA, aptamers, and ribosomes to accomplish targeted delivery...
  55. The Structural Basis of Protein Biogenesis
    Christopher W Akey; Fiscal Year: 2012
    ..PUBLIC HEALTH RELEVANCE: Protein transport channels that associate with ribosomes mediate essential steps in the biogenesis of many proteins (such as peptide hormones, growth factors, apo-..
  56. Regulators of Osteoblast Protein Synthesis Initiation
    THOMAS LEO MCCARTHY; Fiscal Year: 2013
    ..In cell lysates, TCI suppresses the rate of protein synthesis, and disrupts assembly of heavy polymeric ribosomes. Moreover, another component in ribosome depleted cytoplasmic lysates significantly antagonizes TCI ([unreadable]..
  57. The Architecture and Function of RNPs Required for Ribosome Biogenesis
    Susan J Baserga; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Ribosomes, the cellular powerhouses of translation, are assembled from rRNA, the catalytic moiety, and scores of ribosomal proteins...
  58. Role of ribosome impairments in X-linked Dyskeratosis Congenita pathogenesis
    Davide Ruggero; Fiscal Year: 2013
    ..An outstanding question is how "defected" ribosomes produce specific pathological features...
  59. Yersinia Type III Transport of Yop Proteins into Immune Cells
    Olaf Schneewind; Fiscal Year: 2013
    ..sequence of yopR mRNA, promotes selection of its product as an early substrate, presumably by programming ribosomes for secretion...
  60. Software for Homology Modeling of Ribosomes
    FREDRICK OTIENO SIJENYI; Fiscal Year: 2010
    ..RNA-123 will make it possible to model pathogenic bacterial ribosomes, where no crystal structures currently exist, to exploit them in a timely manner to develop new classes of ..
  61. Functional Consequences of Ribosome Heterogeneity
    WENDY VICTORIA GILBERT; Fiscal Year: 2013
    ..Despite increasing proteomic evidence for the production of growth condition and developmental stage specific ribosomes, the functional consequences of such ribosome 'specializations'have never been rigorously tested...
  62. Assembling an understanding of Ribosome Biogenesis
    Gloria M Culver; Fiscal Year: 2013
    ..many details to be elucidated especially regarding ribosome assembly and its impact the functional capacity of ribosomes. Thus, our work to address biosynthesis of E...
  63. NUCLEIC ACID PROBES OF RIBOSOMAL STRUCTURE AND FUNCTION
    BARRY COOPERMAN; Fiscal Year: 2003
    ..tetracycline, erythromycin and other macrolides, neomycin and other aminoglycosides, and chloramphenicol target ribosomes as their sites of action...
  64. Evaluation of RNA transport elements in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2007
    ..from the nucleus to the cytoplasm, localization of the RNA in specific cellular compartments, association with ribosomes, and translation...
  65. Basonuclin and Ribosome Biogenesis in Mouse Oocyte and Embryo
    Richard M Schultz; Fiscal Year: 2010
    ..Translation of maternal mRNA in early embryo depends on the maternal ribosomes. However, a large portion of the maternal ribosomes is destroyed along with many other mRNAs during oocyte ..
  66. CrPV IRES function and animal virus replication in yeast
    SUNNIE THOMPSON; Fiscal Year: 2006
    ..The properties of the cricket paralysis virus (CrPV) IRES are extraordinary, because this IRES can form 80S ribosomes from purified 40S and 60S subunits in the absence of any initiation factors, tRNAs or GTP...
  67. Pseudouridines, pseudouridine synthases, and ribosomes
    MURRAY DEUTSCHER; Fiscal Year: 2006
    ..inhibited growth was that of RluD, a synthase responsible for 3 psi found at the same place in almost all 50S ribosomes. 50S ribosomes from this strain were highly abnormal, and appeared blocked at some stage of assembly...
  68. CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORA
    MATTHEW SACHS; Fiscal Year: 2009
    ..mechanisms by which a nascent peptide encoded by an upstream open reading frame (uORF) controls the movement of ribosomes on mRNA and regulates gene expression...
  69. GENETIC ANALYSIS OF RIBOSOMAL RNA FUNCTION
    Philip Cunningham; Fiscal Year: 2000
    ..However, physical and biochemical studies, indicate that these residues are unpaired in nontranslating ribosomes. We will test the hypothesis that ribosome function in vivo is dependent upon the ability of these residues to ..
  70. STRUCTURE/FUNCTION OF THE 790 LOOP IN RIBOSOMAL RNA
    Philip Cunningham; Fiscal Year: 2001
    ..the chloramphenicol acetyltransferase (CAT) reporter message is translated exclusively by plasmid encoded ribosomes which cannot translate normal cellular messages...