ArticleJournal of molecular evolution2008
The universal trend of amino acid gain-loss is caused by CpG hypermutability.
Article in Journal of molecular evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 17 citations in OpenAlex.
- A simple method for estimating time-irreversible nucleotide substitution rates in the SARS-CoV-2 genome.NAR genomics and bioinformatics · 2024Article
- Evolution of termination codons of proteins and the TAG-TGA paradox.Scientific reports · 2023Article
- Amino acid exchangeabilities vary across the tree of life.Science advances · 2019Article
- Article
- The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process.Frontiers in microbiology · 2018Article
- Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition.Genome biology and evolution · 2017Article
- Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives.Biology · 2016Article
- The biology of developmental plasticity and the Predictive Adaptive Response hypothesis.The Journal of physiology · 2014Review
- New weighting methods for phylogenetic tree reconstruction using multiple loci.Journal of molecular evolution · 2012Article
- A universal trend among proteomes indicates an oily last common ancestor.PLoS computational biology · 2012Article
- The impact of the organism on its descendants.Genetics research international · 2012Article
- A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes.BMC genomics · 2011Article
- Relationship between amino acid composition and gene expression in the mouse genome.BMC research notes · 2011Article
- Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes.BMC genomics · 2010Article
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the cause of the changes in the amino acid composition of proteins is essential for understanding the evolution of protein functions. Since the early 1970s, it has been known that the frequency of some amino acids in protein sequences is increasing and that of others is decreasing. Recently, it was found that the trends of amino acid changes were similar in 15 taxa representing Bacteria, Archaea, and Eukaryota. However, the cause of this similarity in the trend of the gains and losses of amino acids continued to be debated. Here, we show that this trend of the gain and loss of amino acids can be simply explained by CpG hypermutability. We found that the frequency of amino acids coded by codons with TpG dinucleotides and those with CpA dinucleotides is increasing, while that of amino acids coded by codons with CpG dinucleotides is decreasing. We also found that organisms that lack DNA methyltransferase show different trends of the gain and loss of amino acids. DNA methyltransferase methylates CpG dinucleotides and induces CpG hypermutability. The incorporation of CpG hypermutability into models of protein evolution will improve studies on protein evolution in different organisms.
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