Genetic Code Synonym Quotas and Amino Acid Complexity: Cutting the Cost of Proteins?

Dufton, Mark J.

doi:10.1006/jtbi.1997.0443

Cited by 78 publications

(68 citation statements)

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“…It may be expected that the bias in the use of amino acids that we found would correspond to the avoidance of expensive to produce or scarce amino acids. Dufton (1997) developed an index of amino acid size/complexity based on the molecular weight and the shape of amino acids. We used this index as an indirect estimate of amino acid cost and examined its relationship to expression level.…”

Section: Protein Synthesis and Expression Ratesmentioning

confidence: 99%

The Signature of Selection Mediated by Expression on Human Genes

Urrutia¹,

Hurst²

2003

Genome Res.

234

201

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As the efficacy of natural selection is expected to be a function of population size, in humans it is usually presumed that selection is a weak force and hence that gene characteristics are mostly determined by stochastic forces. In contrast, in species with large population sizes, selection is expected to be a much more effective force. Evidence for this has come from examining how genic parameters vary with expression level, which appears to determine many of a gene's features, such as codon bias, amino acid composition, and size. However, not until now has it been possible to examine whether human genes show the signature of selection mediated by expression level. Here, then, to investigate this issue, we gathered expression data for >10,000 human genes from public data sets obtained by different technologies (SAGE and high-density oligonucleotide chip arrays) and compared them with gene parameters. We find that, even after controlling for regional effects, highly expressed genes code for smaller proteins, have less intronic DNA, and higher codon and amino acid biases. We conclude that, contrary to the usual supposition, human genes show signatures consistent with selection mediated by expression level

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Section: Protein Synthesis and Expression Ratesmentioning

confidence: 99%

The Signature of Selection Mediated by Expression on Human Genes

Urrutia¹,

Hurst²

2003

Genome Res.

234

201

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“…Metabolic constraints on protein structure could include the energetic costs of amino acid biosynthesis (1,(9)(10)(11)(12)(13), the biochemical complexity of synthetic pathways (9,11,12), availability of nutrients (14)(15)(16), and the speed and accuracy of protein synthesis (10,(17)(18)(19)(20). Here, we investigate relationships between metabolic costs of amino acid biosynthesis and proteome-wide patterns of amino acid composition in bacterial cells.…”

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confidence: 99%

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

Akashi

Gojobori²

2002

Proc. Natl. Acad. Sci. U.S.A.

601

605

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Biosynthesis of anEven if a substituted amino acid were truly neutral in a functional sense, it is highly unlikely that factors involved in the synthesis of the protein would render the substitution neutral in the broader sense of the organism's integrated functioning. The substituted amino acid must be present within the cell in equivalent quantity compared with the original amino acid and, indeed, its synthesis or derivation from other molecules and transport into the cell require an equivalent amount of energy output.R. C. Richmond (1)

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“…This feature has been attributed to an adaptive selection of a code, so that errors that misread a codon by one letter would result in minimal effects on the translated protein (Freeland and Hurst 1998;Freeland et al 2000;Gilis et al 2001;Wagner 2005b). Second, amino acids with simple chemical structure tend to have more codons assigned to them (Hasegawa and Miyata 1980;Dufton 1997;Di Giulio 2005).…”

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confidence: 99%

The genetic code is nearly optimal for allowing additional information within protein-coding sequences

Itzkovitz¹,

Alon²

2007

Genome Res.

198

165

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DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These "parallel codes" include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code-minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

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Genetic Code Synonym Quotas and Amino Acid Complexity: Cutting the Cost of Proteins?

Cited by 78 publications

References 0 publications

The Signature of Selection Mediated by Expression on Human Genes

The Signature of Selection Mediated by Expression on Human Genes

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

The genetic code is nearly optimal for allowing additional information within protein-coding sequences

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