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Ratio of membrane proteins in total proteomes of prokaryota

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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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Ratio of membrane proteins to total proteins for randomized proteomes also was found to be constant for all organisms, but the average value was 0.085, which is much smaller than the corresponding value for the real proteomes. (A) The solid green line represents the variation in this ratio for Escherichia coli K12, plotted as a function of the randomized simulation up to the 1000-th step. The dotted green line represents the average of the set of membrane protein/total protein ratios of E. coli K12, from mutation steps 300 to 1000, this value being 0.084. (B) Numbers of membrane proteins at the 400-th mutational step are plotted as a function of the numbers of all proteins coded in total genomes. The solid green line is obtained by least square deviation analysis: y=0.085x, with an R2-value of 0.985. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of the 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 as a green line. Skewness, kurtosis and standard deviation of distribution are 0.177, 3.106 and 0.362, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.
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f2-3_37: Ratio of membrane proteins to total proteins for randomized proteomes also was found to be constant for all organisms, but the average value was 0.085, which is much smaller than the corresponding value for the real proteomes. (A) The solid green line represents the variation in this ratio for Escherichia coli K12, plotted as a function of the randomized simulation up to the 1000-th step. The dotted green line represents the average of the set of membrane protein/total protein ratios of E. coli K12, from mutation steps 300 to 1000, this value being 0.084. (B) Numbers of membrane proteins at the 400-th mutational step are plotted as a function of the numbers of all proteins coded in total genomes. The solid green line is obtained by least square deviation analysis: y=0.085x, with an R2-value of 0.985. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of the 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 as a green line. Skewness, kurtosis and standard deviation of distribution are 0.177, 3.106 and 0.362, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.

Mentions: In the first simulation, the probability of the occurrence of amino acids was set to the constant value of 5%. In Figure 2A, the variation in the membrane protein/total protein ratio is shown as a function of the number of mutational steps for the case of Escherichia coli K12. For clarification purposes, the variation to the 1000-th step is shown. The membrane protein/total protein ratio decreased monotonically until a plateau was reached at around 300 steps of the simulation. Because one step includes 1% of mutation, the appearance of the plateau means that the sequences were completely randomized after about 300 steps. Therefore, a ratio of membrane protein to total protein of about 8% at the plateau must be a characteristic of completely random sequences. The decrease of about 0.15 in Figure 2A by the extensive mutations is much lower than the fluctuation of the ratio. We also estimated the systematic error due to the false positive and false negative prediction by SOSUI system. The result showed that the systematic error is about 0.04 which is much smaller than the change in Figure 2A. Therefore, the decrease of about 0.15 is clearly beyond various types of errors.


Ratio of membrane proteins in total proteomes of prokaryota
Ratio of membrane proteins to total proteins for randomized proteomes also was found to be constant for all organisms, but the average value was 0.085, which is much smaller than the corresponding value for the real proteomes. (A) The solid green line represents the variation in this ratio for Escherichia coli K12, plotted as a function of the randomized simulation up to the 1000-th step. The dotted green line represents the average of the set of membrane protein/total protein ratios of E. coli K12, from mutation steps 300 to 1000, this value being 0.084. (B) Numbers of membrane proteins at the 400-th mutational step are plotted as a function of the numbers of all proteins coded in total genomes. The solid green line is obtained by least square deviation analysis: y=0.085x, with an R2-value of 0.985. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of the 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 as a green line. Skewness, kurtosis and standard deviation of distribution are 0.177, 3.106 and 0.362, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.
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getmorefigures.php?uid=PMC5036657&req=5

f2-3_37: Ratio of membrane proteins to total proteins for randomized proteomes also was found to be constant for all organisms, but the average value was 0.085, which is much smaller than the corresponding value for the real proteomes. (A) The solid green line represents the variation in this ratio for Escherichia coli K12, plotted as a function of the randomized simulation up to the 1000-th step. The dotted green line represents the average of the set of membrane protein/total protein ratios of E. coli K12, from mutation steps 300 to 1000, this value being 0.084. (B) Numbers of membrane proteins at the 400-th mutational step are plotted as a function of the numbers of all proteins coded in total genomes. The solid green line is obtained by least square deviation analysis: y=0.085x, with an R2-value of 0.985. Gray closed triangles and solid line indicate the result of Fig. 1A for comparison. (C) The distribution of the 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 as a green line. Skewness, kurtosis and standard deviation of distribution are 0.177, 3.106 and 0.362, respectively. Gray closed triangles and solid line indicate the result of Fig. 1B for comparison.
Mentions: In the first simulation, the probability of the occurrence of amino acids was set to the constant value of 5%. In Figure 2A, the variation in the membrane protein/total protein ratio is shown as a function of the number of mutational steps for the case of Escherichia coli K12. For clarification purposes, the variation to the 1000-th step is shown. The membrane protein/total protein ratio decreased monotonically until a plateau was reached at around 300 steps of the simulation. Because one step includes 1% of mutation, the appearance of the plateau means that the sequences were completely randomized after about 300 steps. Therefore, a ratio of membrane protein to total protein of about 8% at the plateau must be a characteristic of completely random sequences. The decrease of about 0.15 in Figure 2A by the extensive mutations is much lower than the fluctuation of the ratio. We also estimated the systematic error due to the false positive and false negative prediction by SOSUI system. The result showed that the systematic error is about 0.04 which is much smaller than the change in Figure 2A. Therefore, the decrease of about 0.15 is clearly beyond various types of errors.

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