ArticleBMC genomics2006
Evolution of proteomes: fundamental signatures and global trends in amino acid compositions.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 91 citations in OpenAlex.
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- Proteome Size Is Positively Correlated with Lifespan in Mammals but Negatively Correlated with Lifespan in Birds.Advanced biology · 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
- Prodomain-driven enzyme dimerization: a pH-dependent autoinhibition mechanism that controlsmBio · 2024Article
- Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation.Current research in structural biology · 2024Article
- Main Factors Shaping Amino Acid Usage Across Evolution.Journal of molecular evolution · 2023Review
- Evolutionary analysis of KED-rich proteins in plants.PloS one · 2023Article
- Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2.iScience · 2022Article
- Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids.Frontiers in molecular biosciences · 2022Article
- Low-molecular-weight ligands in plants: role in metal homeostasis and hyperaccumulation.Photosynthesis research · 2021Review
- The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?Life (Basel, Switzerland) · 2021Article
- Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds.BMC evolutionary biology · 2019Article
- Why do eukaryotic proteins contain more intrinsically disordered regions?PLoS computational biology · 2019Article
- Introduction of 'Generalized Genomic Signatures' for the quantification of neighbour preferences leads to taxonomy- and functionality-based distinction among sequences.Scientific reports · 2019Article
- Global pentapeptide statistics are far away from expected distributions.Scientific reports · 2018Article
- Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection.Molecular biology and evolution · 2018Article
- Proteome-wide comparison between the amino acid composition of domains and linkers.BMC research notes · 2018Article
- Article
- Genome Data Exploration Using Correspondence Analysis.Bioinformatics and biology insights · 2016Review
- Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.Genome biology and evolution · 2015Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level.
resultsIn this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are compared with various inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment.
conclusionA simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.
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