Selective Profiling of Ribosomes Associated with Yeast Upf Proteins

Overview

Journal Methods

Specialty Biochemistry

Date 2018 Dec 30

PMID 30593864

Citations 4

Authors

Robin Ganesan

John Leszyk

Allan Jacobson

Affiliations

Soon will be listed here.

Abstract

Ribosomes associated with nonsense-mediated decay factors Upf1, Upf2, or Upf3 were purified by immunoprecipitation, and enrichment and stoichiometry of Upf factors and ribosomal proteins were analyzed by western blot and mass spectrometry. Using a small RNA library preparation protocol that eliminates in-gel RNA and cDNA size selection and incorporates four random nucleotides on each side of the ribosome-protected RNA fragment allowed recovery, detection, and analysis of all size classes of protected fragments from a sample simultaneously.

Citing Articles

Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay.

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Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance.

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References

Hu W, Petzold C, Coller J, Baker K . Nonsense-mediated mRNA decapping occurs on polyribosomes in Saccharomyces cerevisiae. Nat Struct Mol Biol. 2010; 17(2):244-7. PMC: 2840703. DOI: 10.1038/nsmb.1734. View

Razzell W . THE PRECIPITATION OF POLYRIBONUCLEOTIDES WITH MAGNESIUM SALTS AND ETHANOL. J Biol Chem. 1963; 238:3053-7. View

McAlister L, Holland M . Isolation and characterization of yeast strains carrying mutations in the glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem. 1985; 260(28):15013-8. View

Culbertson M . RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet. 1999; 15(2):74-80. DOI: 10.1016/s0168-9525(98)01658-8. View

He F, Ganesan R, Jacobson A . Intra- and intermolecular regulatory interactions in Upf1, the RNA helicase central to nonsense-mediated mRNA decay in yeast. Mol Cell Biol. 2013; 33(23):4672-84. PMC: 3838015. DOI: 10.1128/MCB.01136-13. View

Ajamian L, Abel K, Rao S, Vyboh K, Garcia-de-Gracia F, Soto-Rifo R . HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA. Biomolecules. 2015; 5(4):2808-39. PMC: 4693258. DOI: 10.3390/biom5042808. View

Leeds P, Peltz S, Jacobson A, Culbertson M . The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 1991; 5(12A):2303-14. DOI: 10.1101/gad.5.12a.2303. View

Mendell J, Sharifi N, Meyers J, Martinez-Murillo F, Dietz H . Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet. 2004; 36(10):1073-8. DOI: 10.1038/ng1429. View

Ramani A, Nelson A, Kapranov P, Bell I, Gingeras T, Fraser A . High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biol. 2009; 10(9):R101. PMC: 2768976. DOI: 10.1186/gb-2009-10-9-r101. View

10.

Maderazo A, Belk J, He F, Jacobson A . Nonsense-containing mRNAs that accumulate in the absence of a functional nonsense-mediated mRNA decay pathway are destabilized rapidly upon its restitution. Mol Cell Biol. 2003; 23(3):842-51. PMC: 140708. DOI: 10.1128/MCB.23.3.842-851.2003. View

11.

Metzstein M, Krasnow M . Functions of the nonsense-mediated mRNA decay pathway in Drosophila development. PLoS Genet. 2007; 2(12):e180. PMC: 1756896. DOI: 10.1371/journal.pgen.0020180. View

12.

Yepiskoposyan H, Aeschimann F, Nilsson D, Okoniewski M, Muhlemann O . Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA. 2011; 17(12):2108-18. PMC: 3222124. DOI: 10.1261/rna.030247.111. View

13.

Cui Y, Hagan K, Zhang S, Peltz S . Identification and characterization of genes that are required for the accelerated degradation of mRNAs containing a premature translational termination codon. Genes Dev. 1995; 9(4):423-36. DOI: 10.1101/gad.9.4.423. View

14.

Vilardell J, Warner J . Ribosomal protein L32 of Saccharomyces cerevisiae influences both the splicing of its own transcript and the processing of rRNA. Mol Cell Biol. 1997; 17(4):1959-65. PMC: 232042. DOI: 10.1128/MCB.17.4.1959. View

15.

Rayson S, Arciga-Reyes L, Wootton L, de Torres Zabala M, Truman W, Graham N . A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PLoS One. 2012; 7(2):e31917. PMC: 3284524. DOI: 10.1371/journal.pone.0031917. View

16.

Atkin A, Altamura N, Leeds P, Culbertson M . The majority of yeast UPF1 co-localizes with polyribosomes in the cytoplasm. Mol Biol Cell. 1995; 6(5):611-25. PMC: 301219. DOI: 10.1091/mbc.6.5.611. View

17.

Ingolia N, Brar G, Rouskin S, McGeachy A, Weissman J . The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012; 7(8):1534-50. PMC: 3535016. DOI: 10.1038/nprot.2012.086. View

18.

Ivanov P, Gehring N, Kunz J, Hentze M, Kulozik A . Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways. EMBO J. 2008; 27(5):736-47. PMC: 2265754. DOI: 10.1038/emboj.2008.17. View

19.

Ajamian L, Abrahamyan L, Milev M, Ivanov P, Kulozik A, Gehring N . Unexpected roles for UPF1 in HIV-1 RNA metabolism and translation. RNA. 2008; 14(5):914-27. PMC: 2327365. DOI: 10.1261/rna.829208. View

20.

Johansson M, Jacobson A . Nonsense-mediated mRNA decay maintains translational fidelity by limiting magnesium uptake. Genes Dev. 2010; 24(14):1491-5. PMC: 2904939. DOI: 10.1101/gad.1930710. View