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MBE Advance Access published online on January 23, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj091
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted December 12, 2005

Research Article

Evolution of Circular Permutations in Multi-Domain Proteins

January Weiner 3rd 1 * and Erich Bornberg-Bauer 1

1 Division of Bioinformatics, School of Biological Sciences, University of Münster

* To whom correspondence should be addressed.
January Weiner 3rd, E-mail: january{at}uni-muenster.de


  Abstract

Modular rearrangements play an important role in protein evolution. Functional modules, often tantamount to structural domains or smaller fragments, are in many cases well conserved but reoccur in a different order and across many protein families. The underlying genetic mechanisms are gene duplication, fusion and loss of sequence fragments. As a consequence, the sequential order of domains can be inverted, leading to what is known as circularly permutated proteins. Using a recently developed algorithm we have identified a large number of such rearrangements and analysed their evolutionary history. We searched for examples which have arisen by one of the three postulated mechanisms: independent fusion/fission, duplication/deletion and plasmid mediated cut and paste. We conclude that all three mechanisms can be observed, with the independent fusion/fission being the most frequent. This can be partly attributed to highly mobile domains. Duplication/deletion has been found in modular proteins such as peptide synthases.

Availability: Supplementary material can be found at: http://www.uni-muenster.de/Biologie.Botanik/ebb/projects/cp/

Keywords: Circular permutation; domains; modular evolution; rearrangement.
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