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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.


Flow chart of the simulation of point mutations for total proteomes.
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f8-3_37: Flow chart of the simulation of point mutations for total proteomes.

Mentions: The effect of random point mutations on the ratio of membrane proteins was analyzed for all proteins in the 248 prokaryota. The flow chart of the simulation is shown in Figure 8. The initial sequences are the real amino acid sequences of total proteomes. Mutations are randomly introduced into sequences at the rate of one mutation per 100 residues at each step of the simulation. New amino acids were randomly selected at the position of mutation according to the given probabilities of occurrence of amino acids. Then, at each step of the simulation, we estimated the membrane protein/total protein ratio.


Ratio of membrane proteins in total proteomes of prokaryota
Flow chart of the simulation of point mutations for total proteomes.
© Copyright Policy
Related In: Results  -  Collection

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

f8-3_37: Flow chart of the simulation of point mutations for total proteomes.
Mentions: The effect of random point mutations on the ratio of membrane proteins was analyzed for all proteins in the 248 prokaryota. The flow chart of the simulation is shown in Figure 8. The initial sequences are the real amino acid sequences of total proteomes. Mutations are randomly introduced into sequences at the rate of one mutation per 100 residues at each step of the simulation. New amino acids were randomly selected at the position of mutation according to the given probabilities of occurrence of amino acids. Then, at each step of the simulation, we estimated the membrane protein/total protein ratio.

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.