Abstract
We analyzed the amino acid residues present in the water-soluble and transmembrane proteins of 6 thermophilic and 6 mesophilic species of the domains Archaea and Eubacteria, and characterized them as favorable or unfavorable. The characterization was performed by comparing the observed number of each amino acid residue to the expected number calculated from the percentage of nucleotides present in each gene. Amino acids that were more or less abundant than expected were considered as favorable or unfavorable, respectively. Comparisons of amino acid compositions indicated that the water-soluble proteins were rich in charged residues such as Glu, Asp, Lys, and His, whereas hydrophobic residues such as Trp, Phe, and Leu were abundant in transmembrane proteins. Interestingly, our results found that although the Trp residue was abundant in transmembrane proteins, it was not defined as favorable by our calculations, indicating that increased numbers of a particular amino acid does not necessary indicate it is a favorable residue. Amino acids with high G + C content such as Ala, Gly, and Pro were frequently observed as favorable in species with low G + C content. Comparatively, amino acids with low G + C content such as Phe, Tyr, Lys, Ile, and Met were frequently observed as favorable in species with high G + C content. These are the examples to increase the supply of amino acids than expected. Amino acids with neutral G + C content, i.e., Glu and Asp were favorable in water-soluble proteins from all species analyzed, and Cys was unfavorable both in water-soluble and transmembrane proteins. These results indicate that amino acid compositions are essentially determined by the nucleotide sequence of the genes, and the amino acid content is altered by a deviation from expectation.
Highlights
Proteins can be roughly classified into 2 types: water-soluble proteins and transmembrane proteins
These results indicate that amino acid compositions are essentially determined by the nucleotide sequence of the genes, and the amino acid content is altered by a deviation from expectation
We recently reported that the dinucleotide composition of the genes coding for water-soluble proteins differs from those encoding transmembrane proteins [4]
Summary
Proteins can be roughly classified into 2 types: water-soluble proteins and transmembrane proteins. Water-soluble proteins have more charged residues than transmembrane proteins, and the amino acid compositions differ between the 2 types of proteins. We recently reported that the dinucleotide composition of the genes coding for water-soluble proteins differs from those encoding transmembrane proteins [4]. The genes encoding water-soluble proteins are rich in the purine dimers AA, AG, and GA, whereas those encoding transmembrane proteins are rich in the pyrimidine dimers TT, CT, and TC. This trend was observed in thermophilic and mesophilic species of Archaea and Eubacteria. The AA, AG, and GA dinucleotides are complementary to TT, CT, and TC, this revealed that a simple strategy is utilized to produce water-soluble and transmembrane proteins with distinct characteristics by using the DNA sequences on opposing strands
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