New protein functions in yeast chromosome VIII

Ouzounis, Christos A.; Bork, Peer; Casari, Georg; Sander, Chris

doi:10.1002/pro.5560041121

Cited by 32 publications

(19 citation statements)

References 24 publications

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“…Whether yeast and higher eukaryotes require an equivalent to RRF for cytoplasmic protein synthesis is uncertain: attempts to identify a cytoplasmic eukaryotic RRF have failed, to date. Although a yeast gene encoding a protein very similar to prokaryotic RRF has been identified recently (Ouzounis et al, 1995), the product is probably located in the mitochondrion. Consequently, it is possible that in terms of function eRF3 might be equivalent to RF3 and RRF together.…”

Section: Cell Viability and The Need For Rf3 Or Erf3mentioning

confidence: 99%

Polypeptide chain release factors

Buckingham

Grentzmann

Kisselev

1997

Molecular Microbiology

106

123

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SummaryNewly synthesized polypeptide chains are released from peptidyl-tRNA when the ribosome encounters a stop signal on mRNA. Extra-ribosomal proteins (release factors) play an essential role in this process. Although the termination process was first discovered in the late 1960s, much of the mechanism has remained obscure. However, important steps have recently been made in both prokaryotic and eukaryotic organisms in unlocking the secrets of this vital stage in protein synthesis. In this review we summarize these advances and focus attention on the remaining areas of uncertainty, particularly with respect to the models that have been proposed for the action of the GTP-hydrolysing termination factors in prokaryotes and eukaryotes, i.e. RF3 and eRF3.The codon-specific release factors

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Section: Cell Viability and The Need For Rf3 Or Erf3mentioning

confidence: 99%

Polypeptide chain release factors

Buckingham

Grentzmann

Kisselev

1997

Molecular Microbiology

106

123

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“…Saccharomyces cerevisiae chromosome VIII (Ouzounis et al, 1995) and fragments of mammalian and mouse origin available in public databases reveal the existence of pth genes of the prokaryotic type. Biochemical studies of rabbit reticulocytes, however, have revealed another type of Pth activity, due to a phosphodiesterase which removes the terminal adenosine of tRNA together with the peptide, which appear then to be cleaved in a subsequent step (Gross et al, 1992a, b).…”

Section: Discussionmentioning

confidence: 99%

Suppression of thermosensitive peptidyl-tRNA hydrolase mutation in Escherichia coli by gene duplication

Menez

Rémy²,

Buckingham

2001

Microbiology

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Peptidyl-tRNA hydrolase (Pth) in Escherichia coli is required to recycle tRNA molecules that dissociate from the ribosome as peptidyl-tRNA during protein synthesis. At non-permissive temperatures, strains with a thermosensitive mutation affecting the enzyme accumulate peptidyl-tRNA, cease protein synthesis and die. The rate of reversion of this mutation to thermoresistance varies widely according to the genetic background of the cell and the temperature of selection ; under certain conditions, reversion can occur at rates approaching 10 N3 per cell per generation. In such revertants, a chromosomal pth gene can be replaced by an inactivated gene, restoring thermosensitive growth in most cases. PCR amplification experiments and Southern blots show the presence of both normal and inactivated copies of the gene, demonstrating that gene duplication has occurred in the revertants. Estimation of intracellular peptidyl-tRNA hydrolase by Western blotting confirms this explanation of the mechanism of high-frequency reversion to thermoresistance.

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“…Finally, methods will require careful testing on well-defined benchmark sequences and regular reevaluation as reference genome sequences become more complete. This process has already been undertaken in connection with sequencing of prokaryote (Tomb et al 1997), yeast (Ouzounis et al 1995), and Caenorhabditis elegans (P. Green and L. Hillier, in prep.) genomes.…”

Section: Framework Annotationmentioning

confidence: 99%

GAIA: Framework Annotation of Genomic Sequence

et al. 1998

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As increasing amounts of genomic sequence from many organisms become available, and as DNA sequences become a primary reagent in biologic investigations, the role of annotation as a prospective guide for laboratory experiments will expand rapidly. Here we describe a process of high-throughput, reliable annotation, called framework annotation, which is designed to provide a foundation for initial biologic characterization of previously unexamined sequence. To examine this concept in practice, we have constructed Genome Annotation and Information Analysis (GAIA), a prototype software architecture that implements several elements important for framework annotation. The center of GAIA consists of an annotation database and the associated data management subsystem that forms the software bus along which other components communicate. The schema for this database defines three principal concepts: (1) Entries, consisting of sequence and associated historical data; (2) Features, comprising information of biologic interest; and (3) Experiments, describing the evidence that supports Features. The database permits tracking of annotation results over time, as well as assessment of the reliability of particular results. New framework annotation is produced by CARTA, a set of autonomous sensors that perform automatic analyses and assert results into the annotation database. These results are available via a Web-based query interface that uses graphical Java applets as well as text-based HTML pages to display data at different levels of resolution and permit interactive exploration of annotation. We present results for initial application of framework annotation to a set of test sequences, demonstrating its effectiveness in providing a starting point for biologic investigation, and discuss ways in which the current prototype can be improved. The prototype is available for public use and comment at

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New protein functions in yeast chromosome VIII

Cited by 32 publications

References 24 publications

Polypeptide chain release factors

Polypeptide chain release factors

Suppression of thermosensitive peptidyl-tRNA hydrolase mutation in Escherichia coli by gene duplication

GAIA: Framework Annotation of Genomic Sequence

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