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MBE Advance Access published online on September 15, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh263
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted September 8, 2004

Research Article

A General Tendency for Conservation of Protein Length across Eukaryotic Kingdoms

Daryi Wang 1, Mufen Hsieh 1, and Wen-Hsiung Li 2*

1 Computational and Evolutionary Genomics, Center for Genomics Research, Academia Sinica, Taipei, 115 Taiwan
2 Computational and Evolutionary Genomics, Center for Genomics Research, Academia Sinica, Taipei, 115 Taiwan; Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637

* To whom correspondence should be addressed. E-mail: whli{at}uchicago.edu.


  Abstract

Protein elongation can occur in many ways such as domain duplication or insertion and as recruitment of a transposable element fragment into the coding region, and it is believed to be a general tendency in protein evolution. Indeed, a previous study showed that yeast proteins are, on average, longer than their orthologs in bacteria and in this study we found that proteins in yeast, nematode, Drosophila, human, and Arabidopsis are, on average, longer than their orthologs in Escherichia coli. But surprisingly, we found conservation of protein sequence length across eukaryotic kingdoms. We collected 1252 orthologous proteins from yeast, nematode, Drosophila, human, and Arabidopsis, and found that the total length of these proteins is very similar among the five species and that there is no general tendency for a protein to increase or decrease in length. Furthermore, although paralogous proteins tend to undergo more sequence length changes, there is also no general tendency for length increase. However, proteins that are commonly shared by Drosophila and human but not by yeast are, on average, substantially longer than proteins that are shared by yeast, Drosophila and human. This is a puzzle that begs for an answer.

Keywords: protein evolution; protein length; orthologous proteins; paralogous proteins; eukaryotes.
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