Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

Genome Research - Tập 17 Số 11 - Trang 1572-1585 - 2007
Minglei Wang1, Liudmila S. Yafremava2, Derek Caetano-Anollés3, Jay E. Mittenthal3, Gustavo Caetano‐Anollés4
1Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
2National Center for Supercomputing Applications (NCSA)
3University of Illinois at Urbana Champaign
4Carl R. Woese Institute for Genomic Biology

Tóm tắt

The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages. Functional annotation of FSF along these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes the first organismal divide. Reconstruction of phylogenomic trees of proteomes reflects the timeline of architectural diversification in the emerging lineages. Thus, Archaea undertook a minimalist strategy using only a small subset of the full architectural repertoire and then crystallized into a diversified superkingdom late in evolution. Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya.

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Genome Research

Tập 17 Số 11

1572-1585

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