Literature DB >> 26253963

Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway.

Matthew J Payea1, Michael P Guy1, Eric M Phizicky2.   

Abstract

The rapid tRNA decay (RTD) pathway is a tRNA quality control pathway known to degrade several specific hypomodified or destabilized tRNAs in the yeast Saccharomyces cerevisiae. In this chapter, we describe seven methods for identifying RTD substrates, with a focus on two new approaches: a high-throughput approach that utilizes a suppressor tRNA library, fluorescence-activated cell sorting, and deep sequencing, and has greatly expanded the known range of RTD substrates; and a poison primer extension assay that allows for the measurement of levels of suppressor tRNA variants, even in the presence of highly similar endogenous tRNAs. We also discuss different applications of the use of the high-throughput and poison primer extension methodologies for different problems in tRNA biology.
© 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  High throughput; Poison primer extension; RNA-ID; Rapid tRNA decay; SUP4(oc); Yeast

Mesh：

Substances：

Year:  2015        PMID： 26253963      PMCID： PMC5152761          DOI： 10.1016/bs.mie.2015.03.003

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


  22 in total

1.  Rapid tRNA decay can result from lack of nonessential modifications.

Authors:  Andrei Alexandrov; Irina Chernyakov; Weifeng Gu; Shawna L Hiley; Timothy R Hughes; Elizabeth J Grayhack; Eric M Phizicky
Journal:  Mol Cell       Date:  2006-01-06       Impact factor: 17.970

2.  The yeast HAL2 nucleotidase is an in vivo target of salt toxicity.

Authors:  J R Murguía; J M Bellés; R Serrano
Journal:  J Biol Chem       Date:  1996-11-15       Impact factor: 5.157

3.  Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications.

Authors:  Irina Chernyakov; Melanie A Baker; Elizabeth J Grayhack; Eric M Phizicky
Journal:  Methods Enzymol       Date:  2008       Impact factor: 1.600

4.  An in vitro system for the editing of apolipoprotein B mRNA.

Authors:  D M Driscoll; J K Wynne; S C Wallis; J Scott
Journal:  Cell       Date:  1989-08-11       Impact factor: 41.582

5.  Identification of yeast tRNA Um(44) 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNA(Ser) species.

Authors:  Lakmal Kotelawala; Elizabeth J Grayhack; Eric M Phizicky
Journal:  RNA       Date:  2007-11-19       Impact factor: 4.942

6.  Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.

Authors:  Irina Chernyakov; Joseph M Whipple; Lakmal Kotelawala; Elizabeth J Grayhack; Eric M Phizicky
Journal:  Genes Dev       Date:  2008-04-28       Impact factor: 11.361

7.  The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae.

Authors:  B Bonetti; L Fu; J Moon; D M Bedwell
Journal:  J Mol Biol       Date:  1995-08-18       Impact factor: 5.469

8.  Diversity of tRNA genes in eukaryotes.

Authors:  Jeffrey M Goodenbour; Tao Pan
Journal:  Nucleic Acids Res       Date:  2006-11-06       Impact factor: 16.971

9.  A new yeast poly(A) polymerase complex involved in RNA quality control.

Authors:  Stepánka Vanácová; Jeannette Wolf; Georges Martin; Diana Blank; Sabine Dettwiler; Arno Friedlein; Hanno Langen; Gérard Keith; Walter Keller
Journal:  PLoS Biol       Date:  2005-04-19       Impact factor: 8.029

10.  Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis.

Authors:  Michael P Guy; David L Young; Matthew J Payea; Xiaoju Zhang; Yoshiko Kon; Kimberly M Dean; Elizabeth J Grayhack; David H Mathews; Stanley Fields; Eric M Phizicky
Journal:  Genes Dev       Date:  2014-08-01       Impact factor: 11.361
View more
  1 in total

1.  Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast.

Authors:  Matthew J Payea; Alayna C Hauke; Thareendra De Zoysa; Eric M Phizicky
Journal:  RNA       Date:  2019-10-16       Impact factor: 4.942
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.