NAM7

Summary

Gene Symbol: NAM7
Description: ATP-dependent RNA helicase NAM7
Alias: IFS2, MOF4, SUP113, SUT2, UPF1
Species: Saccharomyces cerevisiae S288c

Top Publications

  1. pmc 5' to 3' mRNA decay factors colocalize with Ty1 gag and human APOBEC3G and promote Ty1 retrotransposition
    James A Dutko
    Laboratory of Molecular Genetics, Wadsworth Center, University at Albany, Albany, NY 12201 2002, USA
    J Virol 84:5052-66. 2010
  2. pmc Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p
    A B Maderazo
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655 0122, USA
    Mol Cell Biol 20:4591-603. 2000
  3. ncbi Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay
    Anthony Gaba
    Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, Oregon 97006, USA
    Mol Cell 20:449-60. 2005
  4. pmc Genetic interactions between [PSI+] and nonstop mRNA decay affect phenotypic variation
    Marenda A Wilson
    Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, 6431 Fannin Street, MSB 1 212, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 102:10244-9. 2005
  5. ncbi Upf1p, a highly conserved protein required for nonsense-mediated mRNA decay, interacts with the nuclear pore proteins Nup100p and Nup116p
    Tara Nazarenus
    University of Nebraska Lincoln, School of Biological Sciences, E146 Beadle Center, Lincoln, Nebraska 68588 0666, USA
    Gene 345:199-212. 2005
  6. pmc Targeting of aberrant mRNAs to cytoplasmic processing bodies
    Ujwal Sheth
    Department of Molecular and Cellular Biology, University of Arizona, Tucson, 85721, USA
    Cell 125:1095-109. 2006
  7. ncbi Overexpression of Upf1p compensates for mitochondrial splicing deficiency independently of its role in mRNA surveillance
    B de Pinto
    Consiglio Nazionale delle Ricerche, Istituto di Biomembrane e Bioenergetica, Bari, Italy
    Mol Microbiol 51:1129-42. 2004
  8. pmc Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense-mediated mRNA decay
    Brian Luke
    Swiss Institute for Experimental Cancer Research ISREC, Ecole Polytechnique Federale de Lausanne EPFL, Lausanne, Switzerland
    Nucleic Acids Res 35:7688-97. 2007
  9. pmc Interaction between Ski7p and Upf1p is required for nonsense-mediated 3'-to-5' mRNA decay in yeast
    Shinya Takahashi
    Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113 0033, Japan
    EMBO J 22:3951-9. 2003
  10. ncbi An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation
    Philip Mitchell
    Wellcome Trust Centre for Cell Biology, Institute for Cell and Molecular Biology, King s Buildings, University of Edinburgh, EH9 3JR, United Kingdom
    Mol Cell 11:1405-13. 2003

Scientific Experts

  • P Mitchell
  • M R Culbertson
  • Svetlana Chabelskaya
  • C A Barnes
  • Allan Jacobson
  • Marcus J O Johansson
  • F He
  • Feng He
  • Tadashi Kawashima
  • Guillaume F Chanfreau
  • Kazushige Kuroha
  • A Jacobson
  • Shakir Sayani
  • Luis A Estrella
  • Shinya Takahashi
  • Carlos I Gonzalez
  • Miles F Wilkinson
  • Roy Parker
  • Anton Khmelinskii
  • Jessie Colin
  • Clarivel Lasalde
  • Xuya Wang
  • Ei Ei Min
  • Yang Zhou
  • Toshiaki Katada
  • Stephanie Kervestin
  • Bessie W Kebaara
  • Zhuo Ma
  • Stephanie Kvas
  • Robin Ganesan
  • Matteo Pellegrini
  • Nadia Amrani
  • Toshifumi Inada
  • Rafael Deliz-Aguirre
  • Kylie D Swisher
  • Isabelle Toesca
  • S W Peltz
  • Shubhendu Ghosh
  • Iván J Cajigas
  • James A Dutko
  • Chunfang Li
  • K Czaplinski
  • Masato Taoka
  • Wei Zheng
  • Audrey L Atkin
  • Brian Luke
  • Hiroyuki Kodama
  • Amanda S Ford
  • Shin Ichi Hoshino
  • Ujwal Sheth
  • Biswadip Das
  • Weirong Wang
  • Y Weng
  • Takeshi Sakuno
  • Yasuhiro Araki
  • Marenda A Wilson
  • Shengbing Huang
  • Anthony Gaba
  • Kristi L Penheiter
  • Tara Nazarenus
  • Shinichiro Enomoto
  • Jason W Harger
  • B de Pinto
  • Tetsuo Kobayashi
  • J P Belk
  • Eva N Rodríguez-Cruz
  • Alexander Gunnarsson
  • François Lacroute
  • Lars M Steinmetz
  • Andrea V Rivera
  • Audrey Brossard
  • Deike J Omnus
  • F Messenguy
  • Bernd Fischer
  • Daniel Kirrmaier
  • Marina Pantazopoulou
  • Wolfgang Huber
  • Per O Ljungdahl
  • Tito Candelli
  • Jason Gabunilas
  • José A González-Feliciano
  • Michael Knop
  • Gwénaël Rabut
  • Chenchen Zhu
  • Alfredo J León
  • Irving E Vega
  • Matthias Meurer
  • Ewa Blaszczak
  • Joseph D Barry
  • Gaëlle Le Dez

Detail Information

Publications66

  1. pmc 5' to 3' mRNA decay factors colocalize with Ty1 gag and human APOBEC3G and promote Ty1 retrotransposition
    James A Dutko
    Laboratory of Molecular Genetics, Wadsworth Center, University at Albany, Albany, NY 12201 2002, USA
    J Virol 84:5052-66. 2010
    ..Together, the results suggest that VLPs assemble in P bodies and that 5' to 3' mRNA decay is essential for the packaging of Ty1 RNA in VLPs...
  2. pmc Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p
    A B Maderazo
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655 0122, USA
    Mol Cell Biol 20:4591-603. 2000
    ..Deletion of UPF1, NMD2, or UPF3 stabilized the can1-100 transcript and promoted can1-100 nonsense suppression...
  3. ncbi Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay
    Anthony Gaba
    Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, Oregon 97006, USA
    Mol Cell 20:449-60. 2005
    ..Improving the D13N uORF initiation context also promoted NMD. Hence, NMD appears to be triggered by increased ribosomal occupancy of the uORF termination codon...
  4. pmc Genetic interactions between [PSI+] and nonstop mRNA decay affect phenotypic variation
    Marenda A Wilson
    Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, 6431 Fannin Street, MSB 1 212, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 102:10244-9. 2005
    ..Such a process would allow periodic sampling of the 3' UTR, which can diverge rapidly, for novel and beneficial protein extensions...
  5. ncbi Upf1p, a highly conserved protein required for nonsense-mediated mRNA decay, interacts with the nuclear pore proteins Nup100p and Nup116p
    Tara Nazarenus
    University of Nebraska Lincoln, School of Biological Sciences, E146 Beadle Center, Lincoln, Nebraska 68588 0666, USA
    Gene 345:199-212. 2005
    ..Finally, we see a genetic interaction between UPF1 and NUP100. The growth of upf1Delta, can1-100 cells is inhibited by canavanine...
  6. pmc Targeting of aberrant mRNAs to cytoplasmic processing bodies
    Ujwal Sheth
    Department of Molecular and Cellular Biology, University of Arizona, Tucson, 85721, USA
    Cell 125:1095-109. 2006
    ..Moreover, Upf1p can target normal mRNAs to P-bodies but not promote their degradation. These observations lead us to propose a new model for NMD wherein two successive steps are used to distinguish normal and aberrant mRNAs...
  7. ncbi Overexpression of Upf1p compensates for mitochondrial splicing deficiency independently of its role in mRNA surveillance
    B de Pinto
    Consiglio Nazionale delle Ricerche, Istituto di Biomembrane e Bioenergetica, Bari, Italy
    Mol Microbiol 51:1129-42. 2004
    In yeast the UPF1, UPF2 and UPF3 genes encode three interacting factors involved in translation termination and nonsense-mediated mRNA decay (NMD). UPF1 plays a central role in both processes...
  8. pmc Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense-mediated mRNA decay
    Brian Luke
    Swiss Institute for Experimental Cancer Research ISREC, Ecole Polytechnique Federale de Lausanne EPFL, Lausanne, Switzerland
    Nucleic Acids Res 35:7688-97. 2007
    ..Overall our findings suggest that NMD is more conserved in evolution than previously thought, and that at least one of the Smg5-7 proteins is conserved in budding yeast...
  9. pmc Interaction between Ski7p and Upf1p is required for nonsense-mediated 3'-to-5' mRNA decay in yeast
    Shinya Takahashi
    Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113 0033, Japan
    EMBO J 22:3951-9. 2003
    ..These data suggest that the activation of 3'-to-5' directed NMD is mediated through the interaction between Upf1p and the Ski7p N domain...
  10. ncbi An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation
    Philip Mitchell
    Wellcome Trust Centre for Cell Biology, Institute for Cell and Molecular Biology, King s Buildings, University of Edinburgh, EH9 3JR, United Kingdom
    Mol Cell 11:1405-13. 2003
    ..We conclude that recognition of NMD substrates by the Upf surveillance complex can target mRNAs to rapid deadenylation and exosome-mediated degradation...
  11. pmc Association of yeast Upf1p with direct substrates of the NMD pathway
    Marcus J O Johansson
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 0122, USA
    Proc Natl Acad Sci U S A 104:20872-7. 2007
    ..we distinguished direct from indirect substrates by virtue of their association with the Saccharomyces cerevisiae Upf1 protein...
  12. pmc Upf1 potentially serves as a RING-related E3 ubiquitin ligase via its association with Upf3 in yeast
    Shinya Takahashi
    Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113 0033, Japan
    RNA 14:1950-8. 2008
    ..The Cys- and His-rich repeated N terminus (CH domain) of Upf1 has been implicated in its binding to Upf2...
  13. pmc The shuttling protein Npl3 promotes translation termination accuracy in Saccharomyces cerevisiae
    Luis A Estrella
    Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
    J Mol Biol 394:410-22. 2009
    ..Together, these results lead us to propose a model in which Npl3p engenders translational fidelity by promoting the remodeling of mRNPs during translation termination...
  14. pmc The role of Upf proteins in modulating the translation read-through of nonsense-containing transcripts
    W Wang
    Department of Molecular Genetics and Microbiology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School and The Cancer Institute of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
    EMBO J 20:880-90. 2001
    The yeast UPF1, UPF2 and UPF3 genes encode trans-acting factors of the nonsense-mediated mRNA decay pathway...
  15. ncbi The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for nonsense-mediated mRNA decay
    C I Gonzalez
    Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854, USA
    Mol Cell 5:489-99. 2000
    ..A mutation in HRP1 that stabilizes nonsense-containing mRNAs abolishes its affinity for the DSE and fails to interact with Upf1p. We present a model describing how Hrp1p marks a transcript for rapid decay...
  16. pmc A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing
    B Rutz
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    EMBO J 19:1873-86. 2000
    ..A combination of ts mutants with a disruption of upf1, a gene involved in nonsense-mediated decay, resulted in a specific synthetic growth phenotype, suggesting that the ..
  17. pmc Upf1 stimulates degradation of the product derived from aberrant messenger RNA containing a specific nonsense mutation by the proteasome
    Kazushige Kuroha
    Department of Molecular Biology, Graduate School of Science, Nagoya University, Chikusa ku, Nagoya 464 8602, Japan
    EMBO Rep 10:1265-71. 2009
    ..Here, we show that a crucial NMD factor, up frameshift 1 protein (Upf1), is required for rapid proteasome-mediated degradation of an aberrant protein (PTC product) derived from a PTC-..
  18. pmc Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations
    Tadashi Kawashima
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095 1569, USA
    RNA 15:2236-47. 2009
    ..In addition, deletion of UPF1 partially suppresses the growth defects associated with the prp17Delta or prp22-1 mutations, demonstrating a ..
  19. pmc Nonsense-mediated mRNA decay maintains translational fidelity by limiting magnesium uptake
    Marcus J O Johansson
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
    Genes Dev 24:1491-5. 2010
    ..Alr1p levels increase because an upstream ORF in ALR1 mRNA targets the transcript for NMD. Our results demonstrate that NMD, at least in yeast, controls Mg(2+) homeostasis and, consequently, translational fidelity...
  20. ncbi RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer
    M R Culbertson
    Laboratory of Genetics, R M Bock Laboratories, University of Wisconsin, Madison 53706, USA
    Trends Genet 15:74-80. 1999
    ..The NMD pathway has a direct impact on hundreds of genetic disorders in the human population, where about a quarter of all known mutations are predicted to trigger NMD...
  21. pmc Testing the faux-UTR model for NMD: analysis of Upf1p and Pab1p competition for binding to eRF3/Sup35p
    Stephanie Kervestin
    CNRS UPR9073 Associated with Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico chimique IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France
    Biochimie 94:1560-71. 2012
    ..We conclude that activation of NMD at a premature termination codon is not solely based on the absence of Pab1p and suggest that a specific recruitment step must commit Upf1p to the process and Upf1p-associated mRNAs to NMD...
  22. pmc The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs
    K Czaplinski
    Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School UMDNJ, USA
    Genes Dev 12:1665-77. 1998
    ..The product of the UPF1 gene is a necessary component of the putative surveillance complex that recognizes and degrades aberrant mRNAs...
  23. pmc Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae
    Shakir Sayani
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
    RNA 18:1563-72. 2012
    ..The presence of these two sequential degradation pathways for unspliced pre-mRNAs underscores the importance of limiting their accumulation and might serve as a fail-safe mechanism to prevent the expression of these nonfunctional RNAs...
  24. pmc Upf1p, Nmd2p, and Upf3p are interacting components of the yeast nonsense-mediated mRNA decay pathway
    F He
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655 0122, USA
    Mol Cell Biol 17:1580-94. 1997
    ..nonsense-containing mRNAs in Saccharomyces cerevisiae is dependent on Upf1p, Nmd2p, and Upf3p, the products of the UPF1, NMD2/UPF2, and UPF3 genes, respectively...
  25. pmc Identification and characterization of mutations in the UPF1 gene that affect nonsense suppression and the formation of the Upf protein complex but not mRNA turnover
    Y Weng
    Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School, University of Medicine, Piscataway 08854, USA
    Mol Cell Biol 16:5491-506. 1996
    ..In the yeast Saccharomyces cerevisiae, the Upf1 protein (Upf1p), which contains a cysteine- and histidine-rich region and nucleoside triphosphate hydrolysis and ..
  26. pmc Genetic and biochemical characterization of mutations in the ATPase and helicase regions of the Upf1 protein
    Y Weng
    Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854, USA
    Mol Cell Biol 16:5477-90. 1996
    ..For the yeast Saccharomyces cerevisiae, the Upf1 protein (Upf1p), which contains a cysteine- and histidine-rich region and nucleoside triphosphate hydrolysis and ..
  27. pmc Interaction between Nmd2p and Upf1p is required for activity but not for dominant-negative inhibition of the nonsense-mediated mRNA decay pathway in yeast
    F He
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655 0122, USA
    RNA 2:153-70. 1996
    ..Rapid turnover of nonsense-containing mRNAs in the yeast Saccharomyces cerevisiae is dependent on the products of the UPF1 (Upf1p), NMD2/UPF2 (Nmd2p) and UPF3 (Upf3p) genes...
  28. pmc The pre-mRNA retention and splicing complex controls tRNA maturation by promoting TAN1 expression
    Yang Zhou
    Department of Molecular Biology, Umea University, 901 87 Umea, Sweden
    Nucleic Acids Res 41:5669-78. 2013
    ..Our results demonstrate that TAN1 pre-mRNA processing has an unprecedented requirement for RES factors and that the complex controls the formation of ac(4)C in tRNA...
  29. ncbi Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen
    F He
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655 0122
    Genes Dev 9:437-54. 1995
    Rapid turnover of nonsense-containing mRNAs in yeast in dependent on the product of the UPF1 gene (Upf1p)...
  30. pmc Role for Upf2p phosphorylation in Saccharomyces cerevisiae nonsense-mediated mRNA decay
    Weirong Wang
    Department of Biology, University of Puerto Rico, San Juan, PR 00931
    Mol Cell Biol 26:3390-400. 2006
    ..Two conserved proteins essential for NMD, UPF1 and UPF2, are phosphorylated in higher eukaryotes...
  31. pmc Ebs1p, a negative regulator of gene expression controlled by the Upf proteins in the yeast Saccharomyces cerevisiae
    Amanda S Ford
    Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, WI 53706, USA
    Eukaryot Cell 5:301-12. 2006
    ..Finally, EBS1 transcript levels are under the control of nonsense-mediated mRNA decay (NMD), providing the first example of an NMD-sensitive transcript whose protein product influences a step in gene expression required for NMD...
  32. ncbi The GTP-binding release factor eRF3 as a key mediator coupling translation termination to mRNA decay
    Tetsuo Kobayashi
    Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113 0033, Japan
    J Biol Chem 279:45693-700. 2004
    ..the termination-coupled events, eRF3 interacts with poly(A)-binding protein (Pab1) and the surveillance factor Upf1 to mediate normal and nonsense-mediated mRNA decay...
  33. ncbi A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets
    Kristi L Penheiter
    Department of Biochemistry and Molecular Genetics and Molecular Biology Program, University of Colorado, Denver, USA
    Mol Cell 20:213-23. 2005
    ..MAK21 RNA is sensitive to nonsense-mediated decay (NMD), as revealed by its increased abundance in the absence of Upf1. Therefore, although the Paf1C is associated with Pol II at initiation and during elongation, these critical Paf1-..
  34. ncbi Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families
    J De la Cruz
    Instituto de Bioqu mica Vegetal y Fotos ntesis, Centro Isla de la Cartuja, Universidad de Sevilla CSIC, Americo Vespucio s n, 41092 Sevilla, Spain
    Trends Biochem Sci 24:192-8. 1999
    ..Recent progress in the functional analysis of various family members has given new insights into, and confirmed the significance of these proteins for, most cellular RNA metabolic processes...
  35. pmc Protein quality control at the inner nuclear membrane
    Anton Khmelinskii
    Zentrum für Molekulare Biologie der Universität Heidelberg ZMBH, DKFZ ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
    Nature 516:410-3. 2014
    ..We show that the Asi ubiquitin ligase is involved in degradation of mislocalized integral membrane proteins, thus acting to maintain and safeguard the identity of the INM...
  36. doi Roadblock termination by reb1p restricts cryptic and readthrough transcription
    Jessie Colin
    Centre de Genetique Moleculaire, CNRS UPR3404, 91190 Gif sur Yvette, France
    Mol Cell 56:667-80. 2014
    ..This work demonstrates the importance of roadblock termination for controlling pervasive transcription and preventing transcription through gene regulatory regions. ..
  37. pmc Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae
    Tadashi Kawashima
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
    PLoS Genet 10:e1004249. 2014
    ..cerevisiae but masked by RNA degradation and that the use of alternative splice sites in this organism is mostly aimed at controlling transcript levels rather than increasing proteome diversity. ..
  38. pmc Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1
    Clarivel Lasalde
    Department of Biology, University of Puerto Rico Rio Piedras Campus, San Juan, PR, Department of Reproductive Medicine, University of California, San Diego, CA, Department of Biochemistry, University of Puerto Rico Medical Sciences Campus, San Juan, PR and Molecular Sciences Research Building, San Juan, PR
    Nucleic Acids Res 42:1916-29. 2014
    ..A central component of the NMD pathway is Upf1, an RNA-dependent ATPase and helicase...
  39. pmc Intra- and intermolecular regulatory interactions in Upf1, the RNA helicase central to nonsense-mediated mRNA decay in yeast
    Feng He
    Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Mol Cell Biol 33:4672-84. 2013
    ..the stability and translational fidelity of nonsense-containing mRNAs are controlled by the group I RNA helicase Upf1 and the proteins it interacts with, Upf2 and Upf3...
  40. pmc The Upf factor complex interacts with aberrant products derived from mRNAs containing a premature termination codon and facilitates their proteasomal degradation
    Kazushige Kuroha
    From the Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980 8578 and
    J Biol Chem 288:28630-40. 2013
    ..These findings suggest that the Upf complex may be recruited to ribosomes in a faux 3'-UTR-dependent manner and then associates with aberrant products to facilitate their degradation by the proteasome. ..
  41. pmc Loss of nonsense mediated decay suppresses mutations in Saccharomyces cerevisiae TRA1
    Stephanie Kvas
    Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London N6A5C1, Canada
    BMC Genet 13:19. 2012
    ..To further define the regulatory interactions of Tra1 we isolated extragenic suppressors of the tra1-L3733A allele...
  42. doi Physiological basis of copper tolerance of Saccharomyces cerevisiae nonsense-mediated mRNA decay mutants
    Xuya Wang
    Department of Biology, Baylor University, Waco, TX 76798, USA
    Yeast 30:179-90. 2013
    ..We found that wild-type (UPF1) and upf1Δ mutants accumulate similar amounts of total copper when grown in medium containing elevated levels of ..
  43. pmc Interactions between Upf1 and the decapping factors Edc3 and Pat1 in Saccharomyces cerevisiae
    Kylie D Swisher
    Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
    PLoS ONE 6:e26547. 2011
    ..Critical factors in NMD include Upf1, Upf2, and Upf3, as well as the decapping enzyme, Dcp2/Dcp1...
  44. pmc Multiple roles for the Ess1 prolyl isomerase in the RNA polymerase II transcription cycle
    Zhuo Ma
    Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, USA
    Mol Cell Biol 32:3594-607. 2012
    ..Thus, Ess1 has direct effects on RNA polymerase transcription by controlling cofactor binding via conformationally induced changes in the CTD and indirect effects by influencing chromatin modification...
  45. pmc Yeast Upf1 CH domain interacts with Rps26 of the 40S ribosomal subunit
    Ei Ei Min
    Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
    RNA 19:1105-15. 2013
    The central nonsense-mediated mRNA decay (NMD) regulator, Upf1, selectively targets nonsense-containing mRNAs for rapid degradation...
  46. pmc Telomere cap components influence the rate of senescence in telomerase-deficient yeast cells
    Shinichiro Enomoto
    Department of Genetics, Cell Biology and Development, University of Minnesota, 6 170 MCB Building, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
    Mol Cell Biol 24:837-45. 2004
    ..Saccharomyces cerevisiae cells lacking components of the nonsense-mediated mRNA decay (NMD) pathway (Upf1,Upf2, or Upf3 proteins), senescence is delayed, with crisis occurring approximately 10 to 25 population doublings ..
  47. pmc Upf1 and Upf2 proteins mediate normal yeast mRNA degradation when translation initiation is limited
    C A Barnes
    Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 26:2433-41. 1998
    ..This nonsense-mediated mRNA decay in the yeast Saccharomyces cerevisiae is mediated by the Upf1 and Upf2 proteins. Yeast mRNAs can also be selectively destabilized by limiting the rate of translation initiation...
  48. ncbi Novel class of nuclear genes involved in both mRNA splicing and protein synthesis in Saccharomyces cerevisiae mitochondria
    E B Asher
    Centre de Génétique Moléculaire du C N R S, Laboratoire propre associé à l Université P et M Curie, Gif sur Yvette, France
    Mol Gen Genet 215:517-28. 1989
    We have cloned three distinct nuclear genes, NAM1, NAM7, and NAM8, which alleviate mitochondrial intron mutations of the cytochrome b and COXI (subunit I of cytochrome oxidase) genes when present on multicopy plasmids...
  49. pmc Accumulation of mRNA coding for the ctf13p kinetochore subunit of Saccharomyces cerevisiae depends on the same factors that promote rapid decay of nonsense mRNAs
    J N Dahlseid
    Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 150:1019-35. 1998
    ..Four genes, UPF1, UPF2, UPF3, and ICK1, were represented among extragenic suppressors of ctf13-30...
  50. pmc Translational competence of ribosomes released from a premature termination codon is modulated by NMD factors
    Shubhendu Ghosh
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655 0122, USA
    RNA 16:1832-47. 2010
    ..addition to their well-documented roles in the promotion of nonsense-mediated mRNA decay (NMD), yeast Upf proteins (Upf1, Upf2/Nmd2, and Upf3) also manifest translational regulatory functions, at least in vitro, including roles in ..
  51. doi Copper tolerance of Saccharomyces cerevisiae nonsense-mediated mRNA decay mutants
    Rafael Deliz-Aguirre
    Department of Biology, Baylor University, Waco, TX 76798 7388, USA
    Curr Genet 57:421-30. 2011
    ....
  52. pmc Cryptic transcription mediates repression of subtelomeric metal homeostasis genes
    Isabelle Toesca
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 7:e1002163. 2011
    ....
  53. pmc Overexpression of truncated Nmd3p inhibits protein synthesis in yeast
    J P Belk
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655 0122, USA
    RNA 5:1055-70. 1999
    ..Our data suggest that Nmd3p has a role in the formation, function, or maintenance of the 60S ribosomal subunit and may provide a link for Upf1p to 80S monosomes...
  54. pmc Temperature-sensitive mutations in the Saccharomyces cerevisiae MRT4, GRC5, SLA2 and THS1 genes result in defects in mRNA turnover
    D Zuk
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
    Genetics 153:35-47. 1999
    ..The growth and mRNA decay defects of ts942 (grc5) cells were suppressed by overexpression of the NMD3 gene, encoding a protein shown to participate in a two-hybrid interaction with the nonsense-mediated decay protein Upf1p...
  55. pmc The role of nuclear cap binding protein Cbc1p of yeast in mRNA termination and degradation
    B Das
    Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA
    Mol Cell Biol 20:2827-38. 2000
    ..CBP80 and CBP20 subunits of the nuclear cap binding complex, respectively, or by deletion of the nonessential gene UPF1, which encodes a major component of the mRNA surveillance complex...
  56. pmc An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes
    Masato Taoka
    Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1 1, Hachioji shi, Tokyo 192 0397, Japan
    Nucleic Acids Res 37:e140. 2009
    ....
  57. pmc Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs
    F He
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655 0122, USA
    Mol Cell Biol 21:1515-30. 2001
    ..the NMD factors, we analyzed the mRNA decay phenotypes of yeast strains containing deletions of DCP1 or XRN1 and UPF1, NMD2, or UPF3...
  58. pmc Nonsense-mediated decay of ash1 nonsense transcripts in Saccharomyces cerevisiae
    Wei Zheng
    Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 180:1391-405. 2008
    ..Overall, our results suggest a model in which ash1 mRNAs are insensitive to NMD while translation is repressed during transport but become sensitive once repression is relieved...
  59. pmc Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing
    A T Bond
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655 0122, USA
    Mol Cell Biol 21:7366-79. 2001
    ....
  60. ncbi Role of RNA surveillance proteins Upf1/CpaR, Upf2 and Upf3 in the translational regulation of yeast CPA1 gene
    F Messenguy
    Institut de Recherches Microbiologiques J M Wiame and Laboratoire de Microbiologie de l Université Libre de Bruxelles, Avenue Emile Gryzon 1, 1070 Brussels, Belgium
    Curr Genet 41:224-31. 2002
    ..In this work, we show that the CPAR gene is identical to the UPF1 gene, encoding a protein responsible for the premature termination step of RNA surveillance by nonsense-mediated ..
  61. pmc Inactivation of NMD increases viability of sup45 nonsense mutants in Saccharomyces cerevisiae
    Svetlana Chabelskaya
    Department of Genetics and Breeding, St Petersburg State University, Universitetskaya emb, 7 9, 199034, St Petersburg, Russia
    BMC Mol Biol 8:71. 2007
    ..termination factors eRF1 (Sup45) and eRF3 (Sup35) participate not only in the last step of protein synthesis but also in mRNA degradation and translation initiation via interaction with such proteins as Pab1, Upf1, Upf2 and Upf3.
  62. ncbi The role of N-terminal domain of translational release factor eRF3 for the control of functionality and stability in S. cerevisiae
    Hiroyuki Kodama
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 12:639-50. 2007
    ..These findings suggest that NED functions to switch the functional mode of eRF3 depending on the nature of binding factors...
  63. pmc Mutant LYS2 mRNAs retained and degraded in the nucleus of Saccharomyces cerevisiae
    Biswadip Das
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 103:10871-6. 2006
    ..Furthermore, this "retention signal" causing susceptibility to DRN is lost by altering one of the base pairs, establishing that mRNAs susceptible and unsusceptible to DRN can be attributed to a single nucleotide in the proper context...
  64. pmc Evidence against a direct role for the Upf proteins in frameshifting or nonsense codon readthrough
    Jason W Harger
    Department of Cell Biology and Molecular Genetics, 2135 Microbiology Building, University of Maryland, College Park, MD 20742, USA
    RNA 10:1721-9. 2004
    ..The demonstration that upf sui1 double mutants are synthetically lethal demonstrates an important functional interaction between the NMD and translation initiation pathway...
  65. pmc Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing
    Shengbing Huang
    Department of Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
    Proc Natl Acad Sci U S A 102:13410-5. 2005
    ..The predicted gene products that are affected in three other mutants (nam7, msh2, and rtt106) have not been implicated previously in silencing...