Skip Navigation



MBE Advance Access published online on September 13, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl117
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
23/12/2444    most recent
msl117v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Wang, M.
Right arrow Articles by Caetano-Anollés, G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wang, M.
Right arrow Articles by Caetano-Anollés, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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 September 8, 2006

Research Article

Global Phylogeny Determined by the Combination of Protein Domains in Proteomes

Minglei Wang 1 and Gustavo Caetano-Anollés 1 *

1 Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

* To whom correspondence should be addressed.
Gustavo Caetano-Anollés, E-mail: gca{at}uiuc.edu


  Abstract

The majority of proteins consist of multiple domains that are either repeated or combined in defined order. In this study, we survey the combination of protein domains defined at fold and fold superfamily levels in 185 genomes belonging to organisms that have been fully sequenced and introduce a method that reconstructs rooted phylogenomic trees from the content and arrangement of domains in proteins at a genomic level. We find that the majority of domain combinations were unique to Archaea, Bacteria or Eukarya, suggesting most combinations originated after life had diversified. Domain-repeat and domain repeat within multi-domain proteins increased notably in eukaryotes, mainly at the expense of single-domain and domain-pair proteins. This increased was mostly confined to Metazoa. We also find an unbalanced sharing of domain combinations that suggests Eukarya is more closely related to Bacteria than to Archaea, an observation that challenges the widely assumed eukaryote-archaebacterial sisterhood relationship. The occurrence and abundance of the molecular repertoire (interactome) of domain combinations was used to generate phylogenomic trees. These global interactome-based phylogenies described organismal histories satisfactorily, revealing the tripartite nature of life, and supporting controversial evolutionary patterns, such as the Coelomata hypothesis, the grouping of plants and animals, and the Gram-positive origin of bacteria. Results suggest strongly that the process of domain combination is not random but curved by evolution, rejecting the null hypothesis of domain modules combining in the absence of natural selection or an optimality criterion.

Keywords: protein domains; evolution; phylogenomics; combinations.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
M. K. Basu, L. Carmel, I. B. Rogozin, and E. V. Koonin
Evolution of protein domain promiscuity in eukaryotes
Genome Res., March 1, 2008; 18(3): 449 - 461.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
K. Forslund, A. Henricson, V. Hollich, and E. L. L. Sonnhammer
Domain Tree-Based Analysis of Protein Architecture Evolution
Mol. Biol. Evol., February 1, 2008; 25(2): 254 - 264.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. Wang, L. S. Yafremava, D. Caetano-Anolles, J. E. Mittenthal, and G. Caetano-Anolles
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
Genome Res., November 1, 2007; 17(11): 1572 - 1585.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.