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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.

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The average membrane protein/total protein ratio for randomized proteomes, using the amino acid compositions observed in the real proteomes, was 0.22. (A) The solid red line represents the variation of this ratio for the case of Escherichia coli K12. A dotted green line represents the average the set of membrane protein/total protein ratios in the simulation of the point mutations for the proteome of E. coli K12, this value being 0.247. The result of the simulation in Fig. 2A is shown with solid and dotted gray lines for comparison. (B) Numbers of membrane proteins at the 400-th mutational step is plotted as a function of the numbers of total proteins. The solid orange line was obtained by the least square deviation analysis: y=0.218x, with an R2-value of 0.891. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of deviation from the constant ratio at the 400-th mutational step is shown for all organisms. A Gaussian distribution fitted to the data points is represented by an orange line. Skewness, kurtosis and standard deviation of distribution are −0.040, 3.897 and 1.715, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.
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f3-3_37: The average membrane protein/total protein ratio for randomized proteomes, using the amino acid compositions observed in the real proteomes, was 0.22. (A) The solid red line represents the variation of this ratio for the case of Escherichia coli K12. A dotted green line represents the average the set of membrane protein/total protein ratios in the simulation of the point mutations for the proteome of E. coli K12, this value being 0.247. The result of the simulation in Fig. 2A is shown with solid and dotted gray lines for comparison. (B) Numbers of membrane proteins at the 400-th mutational step is plotted as a function of the numbers of total proteins. The solid orange line was obtained by the least square deviation analysis: y=0.218x, with an R2-value of 0.891. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of deviation from the constant ratio at the 400-th mutational step is shown for all organisms. A Gaussian distribution fitted to the data points is represented by an orange line. Skewness, kurtosis and standard deviation of distribution are −0.040, 3.897 and 1.715, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.

Mentions: The second simulation also introduced random mutations, but used the amino acid compositions of the real proteomes. Figure 3A shows the variation in the membrane protein/total protein ratio for the E. coli K12 proteome, starting from the real sequences to the 1000-th mutational step. The result of the simulation presented in Figure 3A is clearly different from that shown in Figure 2A. The membrane protein/total protein ratio in the simulation based on the amino acid composition of the real proteome was nearly constant throughout the entire simulation process. Figure 3B show the numbers of predicted membrane proteins at the 400-th step of mutation for every organism as a function of the numbers of proteins in the proteomes, while Figure 3C is the distribution of the deviation from the average value of the membrane protein/total protein ratio. Surprisingly, the membrane protein/total protein ratio for the sequences that were randomized starting from the amino acid compositions of the real proteomes was nearly the same as that of the real proteomes, suggesting that the natural selection in the real organisms dose not influence the ratio so much. Moreover, the distribution of the deviation for these random sequences was also the same as that of the real proteomes. Taken together, these results revealed that the membrane protein/total protein ratio and the standard deviation depend on the amino acid compositions. Furthermore, the membrane protein/total protein ratio in the real proteomes seems to be determined by the amino acid composition.


Ratio of membrane proteins in total proteomes of prokaryota
The average membrane protein/total protein ratio for randomized proteomes, using the amino acid compositions observed in the real proteomes, was 0.22. (A) The solid red line represents the variation of this ratio for the case of Escherichia coli K12. A dotted green line represents the average the set of membrane protein/total protein ratios in the simulation of the point mutations for the proteome of E. coli K12, this value being 0.247. The result of the simulation in Fig. 2A is shown with solid and dotted gray lines for comparison. (B) Numbers of membrane proteins at the 400-th mutational step is plotted as a function of the numbers of total proteins. The solid orange line was obtained by the least square deviation analysis: y=0.218x, with an R2-value of 0.891. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of deviation from the constant ratio at the 400-th mutational step is shown for all organisms. A Gaussian distribution fitted to the data points is represented by an orange line. Skewness, kurtosis and standard deviation of distribution are −0.040, 3.897 and 1.715, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.
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f3-3_37: The average membrane protein/total protein ratio for randomized proteomes, using the amino acid compositions observed in the real proteomes, was 0.22. (A) The solid red line represents the variation of this ratio for the case of Escherichia coli K12. A dotted green line represents the average the set of membrane protein/total protein ratios in the simulation of the point mutations for the proteome of E. coli K12, this value being 0.247. The result of the simulation in Fig. 2A is shown with solid and dotted gray lines for comparison. (B) Numbers of membrane proteins at the 400-th mutational step is plotted as a function of the numbers of total proteins. The solid orange line was obtained by the least square deviation analysis: y=0.218x, with an R2-value of 0.891. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of deviation from the constant ratio at the 400-th mutational step is shown for all organisms. A Gaussian distribution fitted to the data points is represented by an orange line. Skewness, kurtosis and standard deviation of distribution are −0.040, 3.897 and 1.715, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.
Mentions: The second simulation also introduced random mutations, but used the amino acid compositions of the real proteomes. Figure 3A shows the variation in the membrane protein/total protein ratio for the E. coli K12 proteome, starting from the real sequences to the 1000-th mutational step. The result of the simulation presented in Figure 3A is clearly different from that shown in Figure 2A. The membrane protein/total protein ratio in the simulation based on the amino acid composition of the real proteome was nearly constant throughout the entire simulation process. Figure 3B show the numbers of predicted membrane proteins at the 400-th step of mutation for every organism as a function of the numbers of proteins in the proteomes, while Figure 3C is the distribution of the deviation from the average value of the membrane protein/total protein ratio. Surprisingly, the membrane protein/total protein ratio for the sequences that were randomized starting from the amino acid compositions of the real proteomes was nearly the same as that of the real proteomes, suggesting that the natural selection in the real organisms dose not influence the ratio so much. Moreover, the distribution of the deviation for these random sequences was also the same as that of the real proteomes. Taken together, these results revealed that the membrane protein/total protein ratio and the standard deviation depend on the amino acid compositions. Furthermore, the membrane protein/total protein ratio in the real proteomes seems to be determined by the amino acid composition.

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.


Related in: MedlinePlus