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Ratio of membrane proteins in total proteomes of prokaryota

View Article: PubMed Central - PubMed

ABSTRACT

The numbers of membrane proteins in the current genomes of various organisms provide an important clue about how the protein world has evolved from the aspect of membrane proteins. Numbers of membrane proteins were estimated by analyzing the total proteomes of 248 prokaryota, using the SOSUI system for membrane proteins (Hirokawa et al., Bioinformatics, 1998) and SOSUI-signal for signal peptides (Gomi et al., CBIJ, 2004). The results showed that the ratio of membrane proteins to total proteins in these proteomes was almost constant: 0.228. When amino acid sequences were randomized, setting the probability of occurrence of all amino acids to 5%, the membrane protein/total protein ratio decreased to about 0.085. However, when the same simulation was carried out, but using the amino acid composition of the above proteomes, this ratio was 0.218, which is nearly the same as that of the real proteomic systems. This fact is consistent with the birth, death and innovation (BDI) model for membrane proteins, in which transmembrane segments emerge and disappear in accordance with random mutation events.

No MeSH data available.


Ratio of membrane proteins to total proteins (A) and the distribution of the deviation from this constant ratio (B) are shown for five sets of proteomes of varying amino acid compositions. The values at the 400-th mutational step of the simulations were used for the analysis. (A) The average membrane protein/total protein ratio decreased in accordance with the decrease in the contribution of the amino acid composition from the real proteomes. The factor α in equation (5), which represents the contribution of the real proteomes, was varied in order to study the relationship between the membrane protein/total protein ratio and the amino acid composition. The results for α values 0.00, 0.25, 0.50, 0.75 and 1.00 are represented by red, orange, green, sky-blue and blue lines, respectively. The average ratios for α values 0.00, 0.25, 0.50, 0.75 and 1.00 were 0.218, 0.183, 0.148, 0.114 and 0.085, respectively, and the corresponding R2-values were 0.891, 0.930, 0.959, 0.981 and 0.985, respectively. (B) Distributions of deviation from these (essentially constant) ratios are shown for α values 0.00, 0.25, 0.50, 0.75 and 1 by the corresponding colors to the graph of (A). All of the distributions could be fitted well with a Gaussian distribution, and the values of the standard deviations increased gradually in accordance with the increase in α: standard deviations of 0.359, 0.465, 0.864, 1.251 and 2.038 were observed for α values 0.00, 0.25, 0.50, 0.75 and 1, respectively. (C) The average membrane protein/total protein ratio and the standard deviation of the distribution from the average ratio are plotted as a function of the factor α of the real proteomes to the amino acid compositions. Membrane protein ratio and standard deviation are indicated by the green closed circle and blue closed triangles, respectively. The standard deviation is shown in the logarithmic scale. The observation of a very good correlation indicates that the membrane protein/total protein ratio is determined by the amino acid composition.
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f5-3_37: Ratio of membrane proteins to total proteins (A) and the distribution of the deviation from this constant ratio (B) are shown for five sets of proteomes of varying amino acid compositions. The values at the 400-th mutational step of the simulations were used for the analysis. (A) The average membrane protein/total protein ratio decreased in accordance with the decrease in the contribution of the amino acid composition from the real proteomes. The factor α in equation (5), which represents the contribution of the real proteomes, was varied in order to study the relationship between the membrane protein/total protein ratio and the amino acid composition. The results for α values 0.00, 0.25, 0.50, 0.75 and 1.00 are represented by red, orange, green, sky-blue and blue lines, respectively. The average ratios for α values 0.00, 0.25, 0.50, 0.75 and 1.00 were 0.218, 0.183, 0.148, 0.114 and 0.085, respectively, and the corresponding R2-values were 0.891, 0.930, 0.959, 0.981 and 0.985, respectively. (B) Distributions of deviation from these (essentially constant) ratios are shown for α values 0.00, 0.25, 0.50, 0.75 and 1 by the corresponding colors to the graph of (A). All of the distributions could be fitted well with a Gaussian distribution, and the values of the standard deviations increased gradually in accordance with the increase in α: standard deviations of 0.359, 0.465, 0.864, 1.251 and 2.038 were observed for α values 0.00, 0.25, 0.50, 0.75 and 1, respectively. (C) The average membrane protein/total protein ratio and the standard deviation of the distribution from the average ratio are plotted as a function of the factor α of the real proteomes to the amino acid compositions. Membrane protein ratio and standard deviation are indicated by the green closed circle and blue closed triangles, respectively. The standard deviation is shown in the logarithmic scale. The observation of a very good correlation indicates that the membrane protein/total protein ratio is determined by the amino acid composition.

Mentions: In order to confirm the strong correlation between the amino acid composition and the membrane protein/total protein ratio, we carried out a third simulation, this time changing the amino acid composition according to equation (2). The numbers of membrane proteins after 400 mutational steps for the entire set of organisms are plotted in Figure 5A as a function of the numbers of proteins in the total proteomes. As the fraction of the real amino acid composition decreased, the ratio of membrane proteins to total proteins monotonically decreased (Fig. 5C). In accordance with the change in this ratio, the distribution of the deviation became gradually sharper (Fig. 5B). The distributions of hydrophobic and amphiphilic amino acids changed according to the variation in the fraction of the real amino acid compositions, as shown in Figures 6A and 6B, respectively. These results indicate that the membrane protein/total protein ratio in the simulations is determined by the amino acid compositions through variation of the hydrophobicity and the amphiphilicity, both physicochemical properties.


Ratio of membrane proteins in total proteomes of prokaryota
Ratio of membrane proteins to total proteins (A) and the distribution of the deviation from this constant ratio (B) are shown for five sets of proteomes of varying amino acid compositions. The values at the 400-th mutational step of the simulations were used for the analysis. (A) The average membrane protein/total protein ratio decreased in accordance with the decrease in the contribution of the amino acid composition from the real proteomes. The factor α in equation (5), which represents the contribution of the real proteomes, was varied in order to study the relationship between the membrane protein/total protein ratio and the amino acid composition. The results for α values 0.00, 0.25, 0.50, 0.75 and 1.00 are represented by red, orange, green, sky-blue and blue lines, respectively. The average ratios for α values 0.00, 0.25, 0.50, 0.75 and 1.00 were 0.218, 0.183, 0.148, 0.114 and 0.085, respectively, and the corresponding R2-values were 0.891, 0.930, 0.959, 0.981 and 0.985, respectively. (B) Distributions of deviation from these (essentially constant) ratios are shown for α values 0.00, 0.25, 0.50, 0.75 and 1 by the corresponding colors to the graph of (A). All of the distributions could be fitted well with a Gaussian distribution, and the values of the standard deviations increased gradually in accordance with the increase in α: standard deviations of 0.359, 0.465, 0.864, 1.251 and 2.038 were observed for α values 0.00, 0.25, 0.50, 0.75 and 1, respectively. (C) The average membrane protein/total protein ratio and the standard deviation of the distribution from the average ratio are plotted as a function of the factor α of the real proteomes to the amino acid compositions. Membrane protein ratio and standard deviation are indicated by the green closed circle and blue closed triangles, respectively. The standard deviation is shown in the logarithmic scale. The observation of a very good correlation indicates that the membrane protein/total protein ratio is determined by the amino acid composition.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036657&req=5

f5-3_37: Ratio of membrane proteins to total proteins (A) and the distribution of the deviation from this constant ratio (B) are shown for five sets of proteomes of varying amino acid compositions. The values at the 400-th mutational step of the simulations were used for the analysis. (A) The average membrane protein/total protein ratio decreased in accordance with the decrease in the contribution of the amino acid composition from the real proteomes. The factor α in equation (5), which represents the contribution of the real proteomes, was varied in order to study the relationship between the membrane protein/total protein ratio and the amino acid composition. The results for α values 0.00, 0.25, 0.50, 0.75 and 1.00 are represented by red, orange, green, sky-blue and blue lines, respectively. The average ratios for α values 0.00, 0.25, 0.50, 0.75 and 1.00 were 0.218, 0.183, 0.148, 0.114 and 0.085, respectively, and the corresponding R2-values were 0.891, 0.930, 0.959, 0.981 and 0.985, respectively. (B) Distributions of deviation from these (essentially constant) ratios are shown for α values 0.00, 0.25, 0.50, 0.75 and 1 by the corresponding colors to the graph of (A). All of the distributions could be fitted well with a Gaussian distribution, and the values of the standard deviations increased gradually in accordance with the increase in α: standard deviations of 0.359, 0.465, 0.864, 1.251 and 2.038 were observed for α values 0.00, 0.25, 0.50, 0.75 and 1, respectively. (C) The average membrane protein/total protein ratio and the standard deviation of the distribution from the average ratio are plotted as a function of the factor α of the real proteomes to the amino acid compositions. Membrane protein ratio and standard deviation are indicated by the green closed circle and blue closed triangles, respectively. The standard deviation is shown in the logarithmic scale. The observation of a very good correlation indicates that the membrane protein/total protein ratio is determined by the amino acid composition.
Mentions: In order to confirm the strong correlation between the amino acid composition and the membrane protein/total protein ratio, we carried out a third simulation, this time changing the amino acid composition according to equation (2). The numbers of membrane proteins after 400 mutational steps for the entire set of organisms are plotted in Figure 5A as a function of the numbers of proteins in the total proteomes. As the fraction of the real amino acid composition decreased, the ratio of membrane proteins to total proteins monotonically decreased (Fig. 5C). In accordance with the change in this ratio, the distribution of the deviation became gradually sharper (Fig. 5B). The distributions of hydrophobic and amphiphilic amino acids changed according to the variation in the fraction of the real amino acid compositions, as shown in Figures 6A and 6B, respectively. These results indicate that the membrane protein/total protein ratio in the simulations is determined by the amino acid compositions through variation of the hydrophobicity and the amphiphilicity, both physicochemical properties.

View Article: PubMed Central - PubMed

ABSTRACT

The numbers of membrane proteins in the current genomes of various organisms provide an important clue about how the protein world has evolved from the aspect of membrane proteins. Numbers of membrane proteins were estimated by analyzing the total proteomes of 248 prokaryota, using the SOSUI system for membrane proteins (Hirokawa et al., Bioinformatics, 1998) and SOSUI-signal for signal peptides (Gomi et al., CBIJ, 2004). The results showed that the ratio of membrane proteins to total proteins in these proteomes was almost constant: 0.228. When amino acid sequences were randomized, setting the probability of occurrence of all amino acids to 5%, the membrane protein/total protein ratio decreased to about 0.085. However, when the same simulation was carried out, but using the amino acid composition of the above proteomes, this ratio was 0.218, which is nearly the same as that of the real proteomic systems. This fact is consistent with the birth, death and innovation (BDI) model for membrane proteins, in which transmembrane segments emerge and disappear in accordance with random mutation events.

No MeSH data available.