How Optimized Is the Translational Machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Xuhua Xia
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Salmonella Typhimurium ◽  
Codon Usage ◽  
Translational Efficiency ◽  
Square Root ◽  
Translational Machinery ◽  
Mutual Adaptation ◽  
Trna Species

Abstract The optimization of the translational machinery in cells requires the mutual adaptation of codon usage and tRNA concentration, and the adaptation of tRNA concentration to amino acid usage. Two predictions were derived based on a simple deterministic model of translation which assumes that elongation of the peptide chain is rate-limiting. The highest translational efficiency is achieved when the codon recognized by the most abundant tRNA reaches the maximum frequency. For each codon family, the tRNA concentration is optimally adapted to codon usage when the concentration of different tRNA species matches the square-root of the frequency of their corresponding synonymous codons. When tRNA concentration and codon usage are well adapted to each other, the optimal content of all tRNA species carrying the same amino acid should match the square-root of the frequency of the amino acid. These predictions are examined against empirical data from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae.

Selective cloning of genes encoding RNase H from Salmonella typhimurium, Saccharomyces cerevisiae and Escherichia coli rnh mutant

1991 ◽  
Vol 227 (3) ◽  
pp. 438-445 ◽  
Author(s):  
Mitsuhiro Itaya ◽  
Dorothy McKelvin ◽  
Sunil K. Chatterjie ◽  
Robert J. Crouch
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Salmonella Typhimurium ◽  
Rnase H ◽  
Genes Encoding

scholarly journals Codon usage of highly expressed genes affects proteome-wide translation efficiency

2018 ◽  
Vol 115 (21) ◽  
pp. E4940-E4949 ◽  
Author(s):  
Idan Frumkin ◽  
Marc J. Lajoie ◽  
Christopher J. Gregg ◽  
Gil Hornung ◽  
George M. Church ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Protein Translation ◽  
Translation Efficiency ◽  
Synonymous Codons ◽  
Codon Composition ◽  
Theoretical Predictions ◽  
Highly Expressed Genes

Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed “codon usage bias.” Previous studies have demonstrated that synonymous changes in a coding sequence can exert significantciseffects on the gene’s expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes inEscherichia coli. This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation.

A hierarchy of trans-acting factors modulates translation of an activator of amino acid biosynthetic genes in Saccharomyces cerevisiae

1985 ◽  
Vol 5 (9) ◽  
pp. 2349-2360 ◽  
Author(s):  
A G Hinnebusch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Fusion Transcript ◽  
Transcript Level ◽  
Amino Acid Starvation ◽  
Lacz Fusion ◽  
Recessive Mutation ◽  
Translational Efficiency ◽  
Biosynthetic Genes ◽  
Fusion Enzyme

The GCN4 gene encodes a positive effector of amino acid biosynthetic genes in Saccharomyces cerevisiae. Genetic analysis has suggested that GCN4 is regulated by a hierarchy of interacting positive and negative effectors in response to amino acid starvation. Results presented here for a GCN4-lacZ gene fusion support this regulatory model and suggest that the regulators of GCN4 exert their effects primarily at the level of translation of GCN4 mRNA. Both the GCN2 and GCN3 products appear to stimulate translation of GCN4 mRNA in response to amino acid starvation, because a recessive mutation in either gene blocked derepression of GCN4-lacZ fusion enzyme levels but did not reduce the fusion transcript level relative to that in wild-type cells grown in the same conditions. The GCD1 product appears to inhibit translation of GCN4 mRNA because under certain growth conditions, the gcd1-101 mutation led to derepression of the GCN4-lacZ fusion enzyme level in the absence of any increase in the fusion transcript level. In addition, the gcd1-101 mutation suppressed the low translational efficiency of GCN4-lacZ mRNA observed in gcn2- and gcn3- cells. A deletion of four small open reading frames in the 5' leader of GCN4-lacZ mRNA mimicked the effect of a gcd1 mutation and derepressed translation of the fusion transcript in the absence of either starvation conditions or the GCN2 and GCN3 products. By contrast, in a gcd1- strain, the deletion resulted in little additional increase in the translational efficiency of the fusion transcript. These results suggest that GCD1 mediates the translational repression normally exerted by the GCN4 leader sequences and that GCN2 and GCN3 antagonize these negative elements in response to amino acid starvation. The effects of the trans-acting mutations on the translation of GCN4-lacZ mRNA remained intact even when transcription of the fusion gene was placed under the control of the S. cerevisiae GAL1 transcriptional control element.

GCD11, a negative regulator of GCN4 expression, encodes the gamma subunit of eIF-2 in Saccharomyces cerevisiae

1993 ◽  
Vol 13 (1) ◽  
pp. 506-520
Author(s):  
E M Hannig ◽  
A M Cigan ◽  
B A Freeman ◽  
T G Kinzy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Metal Binding ◽  
Critical Role ◽  
Cross Reactivity ◽  
Translation Initiation Factor ◽  
Negative Regulator ◽  
Initiation Factor ◽  
Translational Efficiency ◽  
Gamma Subunit

The eukaryotic translation initiation factor eIF-2 plays a critical role in regulating the expression of the yeast transcriptional activator GCN4. Mutations in genes encoding the alpha and beta subunits of eIF-2 alter translational efficiency at the GCN4 AUG codon and constitutively elevate GCN4 translation. Mutations in the yeast GCD11 gene have been shown to confer a similar phenotype. The nucleotide sequence of the cloned GCD11 gene predicts a 527-amino-acid polypeptide that is similar to the prokaryotic translation elongation factor EF-Tu. Relative to EF-Tu, the deduced GCD11 amino acid sequence contains a 90-amino-acid N-terminal extension and an internal cysteine-rich sequence that contains a potential metal-binding finger motif. We have identified the GCD11 gene product as the gamma subunit of eIF-2 by the following criteria: (i) sequence identities with mammalian eIF-2 gamma peptides; (ii) increased eIF-2 activity in extracts prepared from cells cooverexpressing GCD11, eIF-2 alpha, and eIF-2 beta; and (iii) cross-reactivity of antibodies directed against the GCD11 protein with the 58-kDa polypeptide present in purified yeast eIF-2. The predicted GCD11 polypeptide contains all of the consensus elements known to be required for guanine nucleotide binding, suggesting that, in Saccharomyces cerevisiae, the gamma subunit of eIF-2 is responsible for GDP-GTP binding.

scholarly journals Genetic studies of class 2 nonsense suppressors inEscherichia coli

1973 ◽  
Vol 22 (3) ◽  
pp. 223-237 ◽  
Author(s):  
M. Anne Rothwell ◽  
Michael H. L. Green ◽  
Bryn A. Bridges
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Inescherichia Coli ◽  
Mapping Data ◽  
Genetic Studies ◽  
Translational Machinery ◽  
The Third ◽  
Amber Suppressor ◽  
Nonsense Suppressor ◽  
Nonsense Suppressors

SUMMARYThree genetically distinct ochre suppressors have been identified in a strain ofEscherichia coliB/r, all of which suppress a tyrosine auxotrophy and classify as class 2 by phage suppression pattern. One ochre suppressor, which was obtained by conversion from a class 2 amber suppressor, and a second ochre suppressor obtained directly from the non-suppressing parent, were found to have separate map locations, though a peculiar phenotype with regard to a leucine auxotrophy is exhibited by strains carrying either suppressor. We suggest that both suppressors correspond to separate genes for glutamine-insertingtRNA. A Leu+mutant of a strain carrying one of these suppressors was studied and was found to contain a further nonsense suppressor having amber-suppressing activity at a reduced level. We suggest that this suppressor might result from a mutation in another part of the translational machinery concerned with glutamine insertion. The third ochre suppressor has no effect on the leucine auxotrophy and mapping data suggest that it may besupL, an ochre suppressor probably inserting a different amino acid, from glutamine.

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