Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species

Bharanidharan, D.; Bhargavi, G. Ramya; Uthanumallian, Kavitha; Gautham, N.

doi:10.1016/j.bbrc.2004.01.129

Cited by 24 publications

(25 citation statements)

References 27 publications

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“…For example, the frequency of Ala, Gly, and Pro residues, which are composed of G + C-rich codons, was increased in genes with high G + C content, whereas the frequency of Ile, Lys, and Asn residues, which are composed of A + T-rich codons, was decreased in genes with high G + C content. This tendency was observed in both water-soluble and transmembrane proteins, and it is consistent with previous findings [10][11][12][13]33]. The percentage of Lys and Ala residues in the water-soluble proteins plotted against G + C contents of genes demonstrated an almost linear relationship for proteins from both thermophiles and mesophiles (Figure 1).…”

Section: Amino Acid Compositionsupporting

confidence: 91%

“…The nucleotide sequences of bacterial genes have species-specific dinucleotide compositions [7][8][9]. Previous studies identified correlations between the nucleotide composition of genes and the amino acid content of proteins on a genome-wide scale [10][11][12]. However, as water-soluble and transmembrane proteins have different amino acid and nucleotide compositions, it is necessary to analyze them separately like Lobry's study [13].…”

Section: Introductionmentioning

confidence: 99%

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Favorable and unfavorable amino acid residues in water-soluble and transmembrane proteins

Nakashima¹,

Yoshihara²,

Kitamura³

2013

JBiSE

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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.

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Section: Amino Acid Compositionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Favorable and unfavorable amino acid residues in water-soluble and transmembrane proteins

Nakashima¹,

Yoshihara²,

Kitamura³

2013

JBiSE

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“…For example, it is worse for stop-codons. Violations of the mean-field approximation for usage of amino acids Arg, Val, Asp, Glu, Ser, and Cys were reported in [22]. In this section we confirm some of these and other observations and perform statistical evaluation of the mean-field codon usage model for its ability to approximate real codon frequency distributions.…”

Section: Validation Of Codon Usage Models 231 Mean-field (Complete supporting

confidence: 76%

The Mystery of Two Straight Lines in Bacterial Genome Statistics

Gorban

Zinovyev

2007

Bull. Math. Biol.

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In special coordinates (codon position-specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon positionspecific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean-field approximation, which is also known as context-free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.

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“…This challenges the idea that arginine and lysine play the same role in thermostability [30]. Therefore, our comparative genomics analysis strongly supports the conclusion that lysine has a particular or even exceptional role in protein stabilization [31].…”

Section: Analysis Of Complete Proteomesmentioning

confidence: 52%

“…Though bias in amino acid composition toward increasing charged residues is well documented in earlier works [29][30][31][43][44][45][46], the difference in the frequencies of arginine and lysine residues has not been explained unequivocally [30,47].…”

Section: Genomic Motivation For the Novel Mechanism Of Thermostabilitymentioning

confidence: 97%

Entropic stabilization of proteins and its proteomic consequences

et al. 2005

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Evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. However, it is sometimes difficult to discern their causes without a clear understanding of underlying physical mechanisms of thermal stabilization of proteins. For example, it is well-known that hyperthermophiles feature a greater proportion of charged residues, but, surprisingly, the excess of positively charged residues is almost entirely due to lysines but not arginines in the majority of hyperthermophilic genomes. Allatom simulations show that lysines have a much greater number of accessible rotamers than arginines of similar degree of burial in folded states of proteins. This finding suggests that lysines would preferentially entropically stabilize the native state. Indeed, we show in computational experiments that arginine-to-lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanism as a complement to electrostatic stabilization in its strategies of thermophilic adaptation, then hyperthermostable organisms would have much greater content of lysines in their proteomes than comparably sized and similarly charged arginines. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias toward arginine-to-lysine replacement in hyperthermophilic organisms and overall much greater content of lysines than arginines in hyperthermophiles. This finding cannot be explained by genomic GC compositional biases or by the universal trend of amino acid gain and loss in protein evolution. We discovered here a novel entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state and demonstrated its immediate proteomic implications. Our study provides an example of how analysis of a fundamental physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why amino acid compositions of hyperthermophilic proteomes are significantly biased toward lysines but not similarly charged arginines.

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Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species

Cited by 24 publications

References 27 publications

Favorable and unfavorable amino acid residues in water-soluble and transmembrane proteins

Favorable and unfavorable amino acid residues in water-soluble and transmembrane proteins

The Mystery of Two Straight Lines in Bacterial Genome Statistics

Entropic stabilization of proteins and its proteomic consequences

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