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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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Time dependences of the hydropathy plots for amino acid sequences during the simulations. Amino acid sequences which RefSeq accession numbers are NP_417851.3 and NP_417093.1 were used for the hydropathy plots of (A) and (B), respectively. Indexes of hydropathy for amino acid sequences were plotted using seven residues windows.
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f4-3_37: Time dependences of the hydropathy plots for amino acid sequences during the simulations. Amino acid sequences which RefSeq accession numbers are NP_417851.3 and NP_417093.1 were used for the hydropathy plots of (A) and (B), respectively. Indexes of hydropathy for amino acid sequences were plotted using seven residues windows.

Mentions: It should be pointed out that amino acid sequences are completely randomized during the simulation of 400 steps. Since we analyze only the existence of transmembrane helices in this work, a single amino acid sequence can change from the membrane protein to the soluble one and vice versa during the simulation. The time dependences of the hydropathy plots for amino acid sequences from E. coli K12, the accession number of RefSeq NP_417851.3 and NP_417093.1, are shown in Figures 4A and 4B, respectively. Figure 4A is an example of the simulation for the uniform amino acid composition (Fig. 2), and Figure 4B is an example of the simulation for the real amino acid composition (Fig. 3). The dynamic transformation of proteins is clearly demonstrated by the examples. This fact indicates that the good correlation between the number of membrane proteins and the total number of proteins in proteomes is not due to the conservation of initial transmembrane regions and that membrane protein/total protein ratio is determined by the dynamical process of the appearance and disappearance of transmembrane regions in the course of the complete randomization of sequences.


Ratio of membrane proteins in total proteomes of prokaryota
Time dependences of the hydropathy plots for amino acid sequences during the simulations. Amino acid sequences which RefSeq accession numbers are NP_417851.3 and NP_417093.1 were used for the hydropathy plots of (A) and (B), respectively. Indexes of hydropathy for amino acid sequences were plotted using seven residues windows.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036657&req=5

f4-3_37: Time dependences of the hydropathy plots for amino acid sequences during the simulations. Amino acid sequences which RefSeq accession numbers are NP_417851.3 and NP_417093.1 were used for the hydropathy plots of (A) and (B), respectively. Indexes of hydropathy for amino acid sequences were plotted using seven residues windows.
Mentions: It should be pointed out that amino acid sequences are completely randomized during the simulation of 400 steps. Since we analyze only the existence of transmembrane helices in this work, a single amino acid sequence can change from the membrane protein to the soluble one and vice versa during the simulation. The time dependences of the hydropathy plots for amino acid sequences from E. coli K12, the accession number of RefSeq NP_417851.3 and NP_417093.1, are shown in Figures 4A and 4B, respectively. Figure 4A is an example of the simulation for the uniform amino acid composition (Fig. 2), and Figure 4B is an example of the simulation for the real amino acid composition (Fig. 3). The dynamic transformation of proteins is clearly demonstrated by the examples. This fact indicates that the good correlation between the number of membrane proteins and the total number of proteins in proteomes is not due to the conservation of initial transmembrane regions and that membrane protein/total protein ratio is determined by the dynamical process of the appearance and disappearance of transmembrane regions in the course of the complete randomization of sequences.

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