Trends of Amino Acid Usage in the Proteins from the Human Genome

Abstract

Correspondence analysis of amino acid usage was applied to 14,815 complete proteins from the human genome. We found that three major factors influence the variability of amino acidic composition of these proteins, explaining, respectively 20.4%, 14.7%, and 9.9% of the total variability. The first trend is strongly correlated with the GC content of first and second codon positions and is also significantly correlated with the GC level of the corresponding flanking regions and introns. Therefore, the main force shaping amino acid usage among human proteins are the compositional constraints determined by the isochore in which each gene is embedded. The second trend correlates with the hydropathy of each protein and with the frequency of beta-strands. Finally, the third trend is strongly associated with the usage of Cys and the frequency of alpha-helices.

Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes

“…The strongest known predictor of amino acid composition at the genomic scale is the GC content of the coding DNA sequences [2,23]. Thus, it is conceivable that the biased amino acid composition (higher ERK ) in endothermic vertebrates is due to GC content variation between the genomes of endothermic and ectothermic vertebrates.…”

“…Purine loading is found in almost all prokaryotes, and is positively correlated with optimal growth temperature [reviewed in [2]]. As biased nucleotide composition can lead to biased amino acid composition [2,23], it is conceivable that the observed elevated ERK levels in endothermic vertebrates may be a consequence of purine loading.…”

Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence

“…That GC-related forces can skew amino acid usage is also evident within genomes. In mammals, a gene's position within the isochore landscape affects the amino acid usage of the corresponding protein [9], reflected in a correlation between the GC usage at silent third sites in codons and at the first two codon sites ( Figure 2). …”

Similarity of currently circulating H1N1 virus with the 2009 pandemic clone: Viability of an imminent pandemic

“…Single linkage cluster analysis on amino acid usage of all HA genes was performed using STATISTICA (version 6.0, published by Statsoft Inc., USA). Since amino acid usage is multivariate in nature, therefore, it is necessary to analyze this data with multivariate statistical techniques i.e., Correspondence analysis (Greenacre, 1984;Sabbía et al, 2007;Basak et al, 2004;Banerjee et al, 2004;Basak and Ghosh, 2006). Major trend in amino acid usage variation among the HA genes was predicted by Correspondence analysis available in CodonW 1.4.2 (Peden, 2000; http://www.molbiol.ox.ac.uk/cu/).…”