ArticleJournal of molecular evolution2007
Selection on synthesis cost affects interprotein amino acid usage in all three domains of life.
Article in Journal of molecular evolution, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 86 citations in OpenAlex.
- Outsourcing of energetically costly amino acids at the origin of animals.Nature communications · 2026Article
- Amino Acid Frequency in the Proteome Is Not Associated With Realised Thermal Limit nor Dietary Niche Breadth in 35 Lepidoptera Species.Ecology and evolution · 2025Article
- Computational investigation of the sequence context of arginine/glycine-rich motifs in the human proteome.BMC genomics · 2025Article
- Proteome Size Is Positively Correlated with Lifespan in Mammals but Negatively Correlated with Lifespan in Birds.Advanced biology · 2025Article
- Does metabolic rate influence genome-wide amino acid composition in the course of animal evolution?Evolution letters · 2025Article
- Disentangling protein metabolic costs in human cells and tissues.PNAS nexus · 2025Article
- Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost.Protein science : a publication of the Protein Society · 2025Article
- Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities.Scientific reports · 2024Article
- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
- Phosphoribosyltransferases and Their Roles in Plant Development and Abiotic Stress Response.International journal of molecular sciences · 2023Review
- Link between Energy Investment in Biosynthesis and Proteostasis: Testing the Cost-Quality Hypothesis in Insects.Insects · 2023Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- Paleoproteomics.Chemical reviews · 2022Review
- Low-molecular-weight ligands in plants: role in metal homeostasis and hyperaccumulation.Photosynthesis research · 2021Review
- Causes and Consequences of Purifying Selection on SARS-CoV-2.Genome biology and evolution · 2021Article
- Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells.Journal of molecular evolution · 2021Article
- Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants.Scientific reports · 2021Article
- Article
- Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean.Genome biology · 2019Article
- Functional Properties of Amino Acid Side Chains as Biomarkers of Extraterrestrial Life.Astrobiology · 2018Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most investigations of the forces shaping protein evolution have focused on protein function. However, cells are typically 50%-75% protein by dry weight, with protein expression levels distributed over five orders of magnitude. Cells may, therefore, be under considerable selection pressure to incorporate amino acids that are cheap to synthesize into proteins that are highly expressed. Such selection pressure has been demonstrated to alter amino acid usage in a few organisms, but whether "cost selection" is a general phenomenon remains unknown. One reason for this is that reliable protein expression level data is not available for most organisms. Accordingly, I have developed a new method for detecting cost selection. This method depends solely on interprotein gradients in amino acid usage. Applying it to an analysis of 43 whole genomes from all three domains of life, I show that selection on the synthesis cost of amino acids is a pervasive force in shaping the composition of proteins. Moreover, some amino acids have different price tags for different organisms--the cost of amino acids is changed for organisms living in hydrothermal vents compared with those living at the sea surface or for organisms that have difficulty acquiring elements such as nitrogen compared with those that do not--so I also investigated whether differences between organisms in amino acid usage might reflect differences in synthesis or acquisition costs. The results suggest that organisms evolve to alter amino acid usage in response to environmental conditions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.