The nucleotide sequence of threonine transfer RNA coded by bacteriophage T4

Guthrie, Christine; Scholla, Clara Ann; H, Yesian; Abelson, John

doi:10.1093/nar/5.6.1833

Cited by 13 publications

(3 citation statements)

References 17 publications

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“…They all correspond to cellular, naturally occurring and fully sequenced tRNAs. tRNAs of phages and viruses were not taken into account, since they are known to adopt the pattern of modification characteristic for their hosts (for examples see refs: 28,29 ). Likewise, information about mutants of wild type tRNA species was considered as redundant and was omitted from this analysis.…”

Section: Locations and Frequencies Of Post-transcriptionally Modifiedmentioning

confidence: 99%

Distribution and frequencies of post-transcriptional modifications in tRNAs

Olchowik²,

et al. 2014

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Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.

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Section: Locations and Frequencies Of Post-transcriptionally Modifiedmentioning

confidence: 99%

Distribution and frequencies of post-transcriptional modifications in tRNAs

Olchowik²,

et al. 2014

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“…Several lines of A evidence, including hybridization to T4 DNA of aminoacylated tRNAs from T4-infected cells (Scherberg & Weiss, 1970), have suggested that T4 codes for an isoleucine acceptor activity. The nucleotide sequences of the other seven T4 tRNAs have now been determined and include species specific for serine (McClain et al, 1975), proline (Seidman et al, 1975), glutamine (Seidman et al, 1974), leucine (Pinkerton et al, 1973), glycine (Barrell et al, 1973;Stahl et al, 1974), arginine (Mazzara et al, 1977), and threonine (Guthrie et al, 1978). We thus conclude that the molecule we have sequenced corresponds to the acceptor activity identified by Scherberg & Weiss (1970) and infer that it is a tRNA!le.…”

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confidence: 66%

Rare transfer ribonucleic acid essential for phage growth. Nucleotide sequence comparison of normal and mutant T4 isoleucine-accepting transfer ribonucleic acid

Guthrie¹,

McClain²

1979

Biochemistry

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One of the eight tRNA species coded by bacteriophage T4 is unique in that (1) it is found in a yield lower by three- to fourfold than that of any other tRNA and (2) while dispensable for growth in standard laboratory hosts, it is essential for phage propagation in a natural isolate of Escherichia coli (strain CT439). We report here the nucleotide sequence of this tRNA and of several mutationally altered forms. The molecule is 77 nucleotides in length and has the anticodon N-A-U. Depending on the pairing properties of the "wobble" nucleotide N, this sequence could correspond to one or more of the isoleucine-specific codons (formula: see text) or to the methionine-specific codon A-U-G. Since a T4-specific acceptor activity for isoleucine which is stimulated in ribosome binding by A-U-A but not A-U-U has been reported previously, we infer that we have sequenced a tRNA Ile species which preferentially recognizes A-U-A. Mutant HA1 is unable to grow in CT439; it produces no tRNA Ile. The primary mutational alteration is a transition four residues from the 5'terminus which converts a C.G to a U.G base pair. The consequences of this lesion can be partially reversed by second-site mutations nearby in the acceptor stem. Unexpectedly, the tRNA Ile synthesized in these revertants still retains two unusual structural features found in the wild-type molecule: the opposition of two Up residues in the amino acid acceptor stem and the opposition of an Ap and a Gp residue in the anticodon stem. Implications of these structual anomalies for a possibly unique physiological role of this minor tRNA species are discussed.

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“…Nuclease digestion to 3‘-mononucleotides thus positions the label on the 5‘-residue adjacent to the original dNTP, and the 32 P-labeled nucleotide is then identified using 2D-TLC. The method was later expanded to analysis of RNA and found application in tRNA studies, where it was used in conjunction with the conserved structures and locations of many nucleotide modifications to derive tRNA sequences from patterns of nearest neighbors (e.g., refs and ). Although this approach could in principle be applied to contemporary problems of characterizing chemically synthesized DNA or RNA, the practicality of the method is limited by several factors.…”

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confidence: 99%

Determination of Nearest Neighbors in Nucleic Acids by Mass Spectrometry

Rozenski

McCloskey

1999

Anal. Chem.

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The identification of nearest-neighbor residues in nucleic acids provides useful constraints on establishment of base composition and sequence and is potentially applicable to a range of structural problems involving synthetic and natural polynucleotides. A new approach to this problem using electrospray ionization tandem mass spectrometry is based on measurement of precursor-product relationships derived from small fragment ions produced in the high-pressure ionization ("nozzle-skimmer") region of the instrument. Measured mass values of dinucleotide or other fragments, which give rise to mononucleotide ions N formed in the collision cell and transmitted by the second mass analyzer, establish the identities of residues adjacent to N. The technique is applicable to RNA and DNA, whether modified, or not, and is demonstrated using modified residues in nucleic acids up to the size of intact tRNA (76-mer). By monitoring of selected ion reaction channels, the method has been extended to LC/MS and to nearest-neighbor determinations directly in oligonucleotide mixtures.

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The nucleotide sequence of threonine transfer RNA coded by bacteriophage T4

Cited by 13 publications

References 17 publications

Distribution and frequencies of post-transcriptional modifications in tRNAs

Distribution and frequencies of post-transcriptional modifications in tRNAs

Rare transfer ribonucleic acid essential for phage growth. Nucleotide sequence comparison of normal and mutant T4 isoleucine-accepting transfer ribonucleic acid

Determination of Nearest Neighbors in Nucleic Acids by Mass Spectrometry

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