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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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Ratio of membrane proteins to total proteins for various organisms was estimated by prediction systems SOSUI and SOSUIsignal, leading to an average constant value of 0.23. (A) Number of membrane proteins is plotted as a function of total ORFs for 248 prokaryota. The solid blue line was obtained by least square deviation analysis: y=0.228x, with an R2-value of 0.933. (B) The distribution of the deviation from the constant ratio calculated by equation (4) is shown for all organisms. A Gaussian distribution fitted to the data points is represented as a solid blue line. Skewness, kurtosis and standard deviation of distribution are 0.347, 2.404 and 1.561, respectively.
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f1-3_37: Ratio of membrane proteins to total proteins for various organisms was estimated by prediction systems SOSUI and SOSUIsignal, leading to an average constant value of 0.23. (A) Number of membrane proteins is plotted as a function of total ORFs for 248 prokaryota. The solid blue line was obtained by least square deviation analysis: y=0.228x, with an R2-value of 0.933. (B) The distribution of the deviation from the constant ratio calculated by equation (4) is shown for all organisms. A Gaussian distribution fitted to the data points is represented as a solid blue line. Skewness, kurtosis and standard deviation of distribution are 0.347, 2.404 and 1.561, respectively.

Mentions: All amino acid sequences from the total genomes of 248 biological organisms were analyzed for estimation of the ratio of membrane proteins to total proteins in total proteomes. The number of membrane proteins is plotted as a function of the number of all proteins for 248 prokaryote organisms in Figure 1A. In this analysis, we first predicted membrane proteins using the software system SOSUI, and then secretory proteins were removed from the resulting membrane protein set by using the signal peptide predictor SOSUIsignal; both predictors are sufficiently accurate for reliable statistical analysis (the accuracy of SOSUI system is better than 95%). The linearity between the numbers of predicted membrane proteins to that of all proteins in the proteomes was surprisingly good, as seen in Figure 1A, and the R2-value of the correlation was 0.933. The coefficient was 0.228, indicating that about a quarter of amino acid sequences code membrane proteins and that the deviation from the average ratio was small for all biological organisms. When the proportionalities for eubacteria and archaea were analyzed independently, the results were nearly the same: the ratio for eubacteria and archaea were 0.228 and 0.229, respectively, and the corresponding R2-values were 0.930 and 0.927. The fact that the membrane protein/total protein ratio is nearly constant for all organisms suggests the existence of a general mechanism for the conservation of the number of membrane proteins.


Ratio of membrane proteins in total proteomes of prokaryota
Ratio of membrane proteins to total proteins for various organisms was estimated by prediction systems SOSUI and SOSUIsignal, leading to an average constant value of 0.23. (A) Number of membrane proteins is plotted as a function of total ORFs for 248 prokaryota. The solid blue line was obtained by least square deviation analysis: y=0.228x, with an R2-value of 0.933. (B) The distribution of the deviation from the constant ratio calculated by equation (4) is shown for all organisms. A Gaussian distribution fitted to the data points is represented as a solid blue line. Skewness, kurtosis and standard deviation of distribution are 0.347, 2.404 and 1.561, respectively.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036657&req=5

f1-3_37: Ratio of membrane proteins to total proteins for various organisms was estimated by prediction systems SOSUI and SOSUIsignal, leading to an average constant value of 0.23. (A) Number of membrane proteins is plotted as a function of total ORFs for 248 prokaryota. The solid blue line was obtained by least square deviation analysis: y=0.228x, with an R2-value of 0.933. (B) The distribution of the deviation from the constant ratio calculated by equation (4) is shown for all organisms. A Gaussian distribution fitted to the data points is represented as a solid blue line. Skewness, kurtosis and standard deviation of distribution are 0.347, 2.404 and 1.561, respectively.
Mentions: All amino acid sequences from the total genomes of 248 biological organisms were analyzed for estimation of the ratio of membrane proteins to total proteins in total proteomes. The number of membrane proteins is plotted as a function of the number of all proteins for 248 prokaryote organisms in Figure 1A. In this analysis, we first predicted membrane proteins using the software system SOSUI, and then secretory proteins were removed from the resulting membrane protein set by using the signal peptide predictor SOSUIsignal; both predictors are sufficiently accurate for reliable statistical analysis (the accuracy of SOSUI system is better than 95%). The linearity between the numbers of predicted membrane proteins to that of all proteins in the proteomes was surprisingly good, as seen in Figure 1A, and the R2-value of the correlation was 0.933. The coefficient was 0.228, indicating that about a quarter of amino acid sequences code membrane proteins and that the deviation from the average ratio was small for all biological organisms. When the proportionalities for eubacteria and archaea were analyzed independently, the results were nearly the same: the ratio for eubacteria and archaea were 0.228 and 0.229, respectively, and the corresponding R2-values were 0.930 and 0.927. The fact that the membrane protein/total protein ratio is nearly constant for all organisms suggests the existence of a general mechanism for the conservation of the number of membrane proteins.

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