tRNAs as regulators of biological processes.

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🔗 View Article (PMC 4052509)

Published in Front Genet on June 11, 2014

Authors

Medha Raina1, Michael Ibba1

Author Affiliations

1: Department of Microbiology, The Ohio State Biochemistry Program, The Ohio State University Columbus, OH, USA ; Center for RNA Biology, The Ohio State University Columbus, OH, USA.

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A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev (2009) 5.04

The N-end rule in bacteria. Science (1991) 4.21

Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol (2009) 4.07

Universality and structure of the N-end rule. J Biol Chem (1989) 3.97

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Life and death in peripheral T cells. Nat Rev Immunol (2007) 3.67

Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes. Proc Natl Acad Sci U S A (1973) 3.52

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Hidden layers of human small RNAs. BMC Genomics (2008) 3.31

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Anticodon nucleases. Trends Biochem Sci (2000) 1.70

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The T box mechanism: tRNA as a regulatory molecule. FEBS Lett (2010) 1.65

RNA polymerase III transcription factor TFIIIC2 is overexpressed in ovarian tumors. Proc Natl Acad Sci U S A (2000) 1.64

Non-coding RNA production by RNA polymerase III is implicated in cancer. Nat Rev Cancer (2008) 1.62

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Do all modifications benefit all tRNAs? FEBS Lett (2010) 1.46

tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea (2012) 1.43

Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells. RNA Biol (2013) 1.43

Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A (2010) 1.42

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Identification of mammalian arginyltransferases that modify a specific subset of protein substrates. Proc Natl Acad Sci U S A (2005) 1.39

GCN1, a translational activator of GCN4 in Saccharomyces cerevisiae, is required for phosphorylation of eukaryotic translation initiation factor 2 by protein kinase GCN2. Mol Cell Biol (1993) 1.38

Bioactive cyclic dipeptides. Peptides (1995) 1.37

The N-end rule in Escherichia coli: cloning and analysis of the leucyl, phenylalanyl-tRNA-protein transferase gene aat. J Bacteriol (1993) 1.36

Broad-spectrum antimicrobial peptide resistance by MprF-mediated aminoacylation and flipping of phospholipids. Mol Microbiol (2011) 1.34

PRT1 of Arabidopsis thaliana encodes a component of the plant N-end rule pathway. Proc Natl Acad Sci U S A (1998) 1.34

Characterization of tRNA-dependent peptide bond formation by MurM in the synthesis of Streptococcus pneumoniae peptidoglycan. J Biol Chem (2007) 1.31

5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics (2013) 1.30

A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo. Genes Dev (2010) 1.30

Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene. J Mol Biol (2004) 1.30

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Synthesis of the L-alanyl-L-alanine cross-bridge of Enterococcus faecalis peptidoglycan. J Biol Chem (2002) 1.24

Adaptation of Pseudomonas aeruginosa to various conditions includes tRNA-dependent formation of alanyl-phosphatidylglycerol. Mol Microbiol (2008) 1.24

Separate domains in GCN1 for binding protein kinase GCN2 and ribosomes are required for GCN2 activation in amino acid-starved cells. EMBO J (2000) 1.24

High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma. Biochem Biophys Res Commun (2009) 1.23

Overexpression of initiator methionine tRNA leads to global reprogramming of tRNA expression and increased proliferation in human epithelial cells. RNA (2013) 1.22

The albonoursin gene Cluster of S noursei biosynthesis of diketopiperazine metabolites independent of nonribosomal peptide synthetases. Chem Biol (2002) 1.21

Structural elements defining elongation factor Tu mediated suppression of codon ambiguity. Nucleic Acids Res (2007) 1.21

Inducible expression, enzymatic activity, and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum. J Biol Chem (2003) 1.13

Synergistic antimicrobial activity of metabolites produced by a nonobligate bacterial predator. Antimicrob Agents Chemother (2003) 1.12

Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog. EMBO J (2006) 1.11