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Open Access Highly Accessed Research article

Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement

Kazuhiro Takemoto12*, Tatsuya Niwa3 and Hideki Taguchi3

Author affiliations

1 PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan

2 Department of Biophysics and Biochemistry, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan

3 Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta 4259-B56, Midori-ku, Yokohama 226-8501, Japan

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Citation and License

BMC Systems Biology 2011, 5:98  doi:10.1186/1752-0509-5-98

Published: 24 June 2011

Abstract

Background

Chaperonins are important in living systems because they play a role in the folding of proteins. Earlier comprehensive analyses identified substrate proteins for which folding requires the chaperonin GroEL/GroES (GroE) in Escherichia coli, and they revealed that many chaperonin substrates are metabolic enzymes. This result implies the importance of chaperonins in metabolism. However, the relationship between chaperonins and metabolism is still unclear.

Results

We investigated the distribution of chaperonin substrate enzymes in the metabolic network using network analysis techniques as a first step towards revealing this relationship, and found that as chaperonin requirement increases, substrate enzymes are more laterally distributed in the metabolic. In addition, comparative genome analysis showed that the chaperonin-dependent substrates were less conserved, suggesting that these substrates were acquired later on in evolutionary history.

Conclusions

This result implies the expansion of metabolic networks due to this chaperonin, and it supports the existing hypothesis of acceleration of evolution by chaperonins. The distribution of chaperonin substrate enzymes in the metabolic network is inexplicable because it does not seem to be associated with individual protein features such as protein abundance, which has been observed characteristically in chaperonin substrates in previous works. However, it becomes clear by considering this expansion process due to chaperonin. This finding provides new insights into metabolic evolution and the roles of chaperonins in living systems.