Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Relationship between G + C in silent sites of codons and amino acid composition of human proteins.

Literature DB >> 8483158

Relationship between G + C in silent sites of codons and amino acid composition of human proteins.

Abstract

We have investigated the relationship between the G + C content of silent (synonymous) sites in codons and the amino acid composition of encoded proteins for approximately 1,600 human genes. There are positive correlations between silent site G + C and the proportions of codons for Arg, Pro, Ala, Trp, His, Gln, and Leu and negative ones for Tyr, Phe, Asn, Ile, Lys, Asp, Thr, and Glu. The median proteins coded by groups of genes that differ in silent-site G + C content also differ in amino acid composition, as do some proteins coded by homologous genes. The pattern of compositional change can be largely explained by directional mutation pressure, the genetic code, and differences in the frequencies of accepted amino acid substitutions; the shifts in protein composition are likely to be selectively neutral.

Entities: Chemical Species

Mesh：

Substances：

Year: 1993 PMID： 8483158 DOI： 10.1007/bf00160475

Source DB: PubMed Journal: J Mol Evol ISSN： 0022-2844 Impact factor: 2.395

35 in total

1. On the genetic basis of variation and heterogeneity of DNA base composition.

Authors: N SUEOKA
Journal: Proc Natl Acad Sci U S A Date: 1962-04-15 Impact factor: 11.205

2. Numerical classification of coding sequences.

Authors: D W Collins; C C Liu; T H Jukes
Journal: Nucleic Acids Res Date: 1992-03-25 Impact factor: 16.971

3. The compositional properties of human genes.

Authors: B Aïssani; G D'Onofrio; D Mouchiroud; K Gardiner; C Gautier; G Bernardi
Journal: J Mol Evol Date: 1991-06 Impact factor: 2.395

4. Compositional constraints and genome evolution.

Authors: G Bernardi; G Bernardi
Journal: J Mol Evol Date: 1986 Impact factor: 2.395

5. The GenBank genetic sequence data bank.

Authors: H S Bilofsky; C Burks
Journal: Nucleic Acids Res Date: 1988-03-11 Impact factor: 16.971

6. Diversity in G + C content at the third position of codons in vertebrate genes and its cause.

Authors: S Aota; T Ikemura
Journal: Nucleic Acids Res Date: 1986-08-26 Impact factor: 16.971

7. Activation of the c-K-ras oncogene in a human pancreas carcinoma.

Authors: H Hirai; T Okabe; Y Anraku; M Fujisawa; A Urabe; F Takaku
Journal: Biochem Biophys Res Commun Date: 1985-02-28 Impact factor: 3.575

8. Cloning and expression of full-length cDNA encoding human vitamin D receptor.

Authors: A R Baker; D P McDonnell; M Hughes; T M Crisp; D J Mangelsdorf; M R Haussler; J W Pike; J Shine; B W O'Malley
Journal: Proc Natl Acad Sci U S A Date: 1988-05 Impact factor: 11.205

Review 9. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.

Authors: W H Li; C I Wu; C C Luo
Journal: Mol Biol Evol Date: 1985-03 Impact factor: 16.240

10. Molecular cloning and the total nucleotide sequence of the human c-Ha-ras-1 gene activated in a melanoma from a Japanese patient.

Authors: T Sekiya; M Fushimi; H Hori; S Hirohashi; S Nishimura; T Sugimura
Journal: Proc Natl Acad Sci U S A Date: 1984-08 Impact factor: 11.205

13 in total

1. Codon usage between genomes is constrained by genome-wide mutational processes.

Authors: Swaine L Chen; William Lee; Alison K Hottes; Lucy Shapiro; Harley H McAdams
Journal: Proc Natl Acad Sci U S A Date: 2004-02-27 Impact factor: 11.205

2. Mutational bias plays an important role in shaping longevity-related amino acid content in mammalian mtDNA-encoded proteins.

Authors: Juan Carlos Aledo; Héctor Valverde; João Pedro de Magalhães
Journal: J Mol Evol Date: 2012-06-30 Impact factor: 2.395

Relationship between G + C in silent sites of codons and amino acid composition of human proteins.

1. On the genetic basis of variation and heterogeneity of DNA base composition.

2. Numerical classification of coding sequences.

3. The compositional properties of human genes.

4. Compositional constraints and genome evolution.

5. The GenBank genetic sequence data bank.

6. Diversity in G + C content at the third position of codons in vertebrate genes and its cause.

7. Activation of the c-K-ras oncogene in a human pancreas carcinoma.

8. Cloning and expression of full-length cDNA encoding human vitamin D receptor.

Review 9. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.

10. Molecular cloning and the total nucleotide sequence of the human c-Ha-ras-1 gene activated in a melanoma from a Japanese patient.

1. Codon usage between genomes is constrained by genome-wide mutational processes.

2. Mutational bias plays an important role in shaping longevity-related amino acid content in mammalian mtDNA-encoded proteins.

3. Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA.

4. Chromatin self-organization by mutation bias.

5. Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes.

6. The translational termination signal database (TransTerm) now also includes initiation contexts.

7. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group.

8. Analysis of expressed sequence tags from calcifying cells of marine coccolithophorid (Emiliania huxleyi).

9. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata.

10. The unique genomic properties of sex-biased genes: insights from avian microarray data.