Comparison of dissimilarity patterns of E coli, yeast and mammalian tRNAs

Steinberg, Sergey V.; Kisselev, Lev L.

doi:10.1016/0300-9084(92)90111-q

Cited by 8 publications

(3 citation statements)

References 25 publications

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“…The other sets of identity determinants which have been uncovered are, for the most part, more complex. Computer analysis of dissimilarity patterns suggests that there may be significant differences between the identity elements in tRNAs of 'prokaryotic' and 'eukaryotic' type [30,36], and this is borne out by the fact that eukaryotic cytosolic tRNAs are often poor substrates for bacterial, chloroplast or (with the exception of imported tRNAs, see below) mitochondrial aminoacyl-tRNA synthetases and vice versa [6,37,39]. One interaction which has been studied in several organisms is the recognition of t R N A l'he by phenylalanyl-tRNA synthetase.…”

Section: Discussionmentioning

confidence: 99%

Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs

et al. 1994

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Alanine and phenylalanine tRNA sequences were amplified by PCR from Arabidopsis thaliana nuclear DNA using degenerate oligonucleotides which introduced specific mutations into the acceptor stem. The aminoacylation of T7 RNA polymerase transcripts of these sequences was investigated in vitro using partially purified bean alanyl- or phenylalanyl-tRNA synthetase. In parallel, the in vivo activity of amber suppressor derivatives of these tRNAs was investigated in transient expression assays in tobacco protoplasts using a beta-glucuronidase (GUS) reporter gene containing a premature amber stop codon. The results show that mutation of the G3:U70 base pair to G3:C70 blocks aminoacylation of plant alanine tRNA, whilst conversion of the G3:C70 pair normally found in plant tRNA(Phe) to G3:U70 enables the mutated tRNA(Phe) to be a good substrate for alanyl-tRNA synthetase and impairs its aminoacylation with phenylalanine. In addition, the amber suppressor derivative of wild-type tRNA(Phe) showed very little suppressor activity in vivo, and was poorly aminoacylated with phenylalanine in vitro, suggesting that the anticodon is a major identity determinant for tRNA(Phe) in plant cells.

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Section: Discussionmentioning

confidence: 99%

Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs

et al. 1994

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“…In order to facilitate a computer analysis, an alignment of sequences is used, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA (5,6). The corresponding numbering system is described in (1).…”

Section: Database Content and Organizationmentioning

confidence: 99%

Compilation of tRNA sequences and sequences of tRNA genes

Sprinzl

Vassilenko

2004

Nucleic Acids Research

1,150

298

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Maintained at the Universität Bayreuth, Bayreuth, Germany, the Compilation of tRNA Sequences and Sequences of tRNA Genes is accessible at the URL http://www.tRNA.uni-bayreuth.de with mirror site located at the Institute of Protein Research, Pushchino, Russia (http://alpha.protres.ru/trnadbase). The compilation is a searchable, periodically updated database of currently available tRNA sequences. The present version of the database contains a new Genomic tRNA Compilation including the sequences of tRNA genes from genomic sequences published up to July 2003. It consists of about 5800 tRNA gene sequences from 111 organisms covering archaea, bacteria, higher and lower eukarya. The former Compilation of tRNA Genes (up to the end of 1998) and the updated Compilation tRNA Sequences (561 entries) are also supported by the new software. The database can be explored by using multiple search criteria and sequence templates. The database provides a service that allows to obtain statistical information on the occurrences of certain bases at given positions of the tRNA sequences. This allows phylogenic studies and search for identity elements in respect to interactions of tRNAs with various enzymes.

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“…The set of tRNA sequences Fourty nine sequences of E. coli tRNAs or their genes were taken from the compilation of tRNA and tRNA gene sequences (12) and aligned as was suggested previously (13). Modified nucleotides were replaced by their precursors.…”

Section: Methodsmentioning

confidence: 99%

Mosaic tile model for tRNA-enzyme recognition

Steinberg

Kisselev

1993

Nucl Acids Res

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An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucleotide and its neighbours as they are defined by the tertiary structure of the molecule. Informational content of each tile is calculated as its probability to occur exclusively in a set of cognate tRNAs. Based on this algorithm the identity sites of E.coli tRNAAIa and tRNAGIn were determined. The results are in a good agreement with the biochemical data and provide new information about identity sites of these tRNAs.

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Comparison of dissimilarity patterns of E coli, yeast and mammalian tRNAs

Cited by 8 publications

References 25 publications

Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs

Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs

Compilation of tRNA sequences and sequences of tRNA genes

Mosaic tile model for tRNA-enzyme recognition

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