Journal ArticleDOI
A universal trend of amino acid gain and loss in protein evolution
I. King Jordan,Fyodor A. Kondrashov,Ivan Adzhubei,Yuri I. Wolf,Eugena V. Koonin,Alexey S. Kondrashov,Shasnil Sunyaev +6 more
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TLDR
Comparison of sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life and phylogenies to polarize amino acid substitutions shows expansion of initially under-represented amino acids apparently continues to this day.Abstract:
A comparison of corresponding sets of proteins encoded by closely related genes from organisms representing all three domains of life (Bacteria, Archaea and Eukaryota) suggests that the order in which the genetic code was assembled over 3.5 billion years ago continues to influence the evolution of proteins today. Across these diverse genomes, evolving proteins have accumulated Cys, Met, His, Ser and Phe, and lost many of their Pro, Ala, Glu and Gly residues. The same nine amino acids are currently accrued or lost in human proteins as shown by analysis of nucleotide polymorphisms. The amino acids with declining frequencies were probably among the first incorporated into the genetic code, and most of those with increasing frequencies were probably recruited late. Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons1,2,3,4. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late5,6,7. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago8,9, apparently continues to this day.read more
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The changing faces of glutathione, a cellular protagonist
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Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
TL;DR: Sequence analyses based on the results imply that foldable sequences with more compact unfolded states are a more recent result of protein evolution.
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Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy
TL;DR: It is concluded that selection on synonymous codon use in E. coli is largely due to selection for translational accuracy, to reduce the costs of both missense and nonsense errors.
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Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins.
Kaavya A Mohanasundaram,Naomi L. Haworth,Mani P Grover,Tamsyn M. Crowley,Andrzej Goscinski,Merridee A. Wouters +5 more
TL;DR: A redox-active disulfide may be introduced into a protein structure by stepwise mutation of two residues in the native sequence to Cys, which is likely to be the cysteine of the CSD which undergoes nucleophilic attack by thioredoxin.
References
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Book ChapterDOI
Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria
TL;DR: The dnaA gene in bacteria was used as an example to show that the amino acid composition of a protein can be dramatically affected by mutational pressure, and that surprisingly, deleting relatively closely-related genera may increase rather than decrease the correlation between genomic GC content and amino Acid composition.