ArticleJournal of molecular evolution2005
Universal sharing patterns in proteomes and evolution of protein fold architecture and life.
Article in Journal of molecular evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Origins and Functional Significance of Eukaryotic Protein Folds.Journal of molecular evolution · 2023Article
- Protein folds as synapomorphies of the tree of life.Evolution; international journal of organic evolution · 2022Article
- The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data.PloS one · 2017Article
- Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.Archaea (Vancouver, B.C.) · 2013Article
- Evolutionary optimization of protein folding.PLoS computational biology · 2013Article
- A general framework of persistence strategies for biological systems helps explain domains of life.Frontiers in genetics · 2013Article
- Review
- The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.BMC evolutionary biology · 2012Article
- Biphasic patterns of diversification and the emergence of modules.Frontiers in genetics · 2012Article
- The enzymatic and metabolic capabilities of early life.PloS one · 2012Article
- The proteomic complexity and rise of the primordial ancestor of diversified life.BMC evolutionary biology · 2011Article
- Small cofactors may assist protein emergence from RNA world: clues from RNA-protein complexes.PloS one · 2011Article
- The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner.Biology direct · 2008Review
- Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world.Genome research · 2007Article
- The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery.Genome biology · 2007Article
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2 authors.
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Abstract
Protein evolution is imprinted in both the sequence and the structure of evolutionary building blocks known as protein domains. These domains share a common ancestry and can be unified into a comparatively small set of folding architectures, the protein folds. We have traced the distribution of protein folds between and within proteomes belonging to Eukarya, Archaea, and Bacteria along the branches of a universal phylogeny of protein architecture. This tree was reconstructed from global fold-usage statistics derived from a structural census of proteomes. We found that folds shared by the three organismal domains were placed almost exclusively at the base of the rooted tree and that there were marked heterogeneities in fold distribution and clear evolutionary patterns related to protein architecture and organismal diversification. These include a relative timing for the emergence of prokaryotes, congruent episodes of architectural loss and diversification in Archaea and Bacteria, and a late and quite massive rise of architectural novelties in Eukarya perhaps linked to multicellularity.
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