MBE Advance Access originally published online on March 18, 2008
Molecular Biology and Evolution 2008 25(6):1113-1119; doi:10.1093/molbev/msn063
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Research Articles |
Emergence of Polyproline II-Like Structure at Early Stages of Experimental Evolution from Random Polypeptides
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* Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
Graduate School of Frontier Science, Osaka University, Suita, Osaka, Japan
Complex Systems Biology Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Suita, Osaka, Japan
E-mail: yomo{at}ist.osaka-u.ac.jp
Accepted for publication February 21, 2008.
To examine whether a primordial functional protein at the early stages of evolution has structural features, we carried out experimental evolution consisting of 25 cycles (generations) of mutation and selection toward DNA-binding function using a random-sequence polypeptide of 139 amino acid residues with no secondary structure as the initial sequence. In each generation, 16 clones were sampled arbitrarily for sequence analysis, and a phylogenetic tree was constructed. Polypeptide evolution proceeded from the initial point on branch I in 2 main directions of branches II and III. The initial and 2 evolved polypeptides (one at the 24th generation on branch III and the other at the 25th generation on branch II) were purified to examine their functional and structural properties. Although binding of the initial polypeptide to the target DNA was not detected by surface plasmon resonance measurements, the 2 evolved polypeptides bound to the DNA with dissociation constants of 1.6 and 1.0 µM, respectively, indicating an increase in affinity during the experimental evolution. Circular dichroism spectra of the evolved polypeptides, but not of the initial polypeptide, showed features characteristic of the polyproline II (PPII)–like structure, a left-handed helical structure commonly found in natural proteins, suggesting that the structure emerged through the experimental evolution. The same structural feature was found in another experimental evolution toward catalytic activity. These results demonstrate that the PPII-like structure is one of the common features that could have appeared in the early evolutionary stages of primordial functional protein.
Key Words: experimental evolution • early evolution • random polypeptide • polyproline II • DNA binding
Takashi Gojobori, Associate Editor