ArticleGenome research2007
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
82 citing papers in PubMed, 140 citations in OpenAlex.
- Universal paralogs provide a window into evolution before the last universal common ancestor.Cell genomics · 2026Review
- A new LUCApedia database for data-driven research on early evolutionary history.Bioinformatics advances · 2026Article
- Phylogeny Building for Structural Phylogenomic Research.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Tracing Molecular Chronologies Onto Growing Biological Networks.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes.Scientific reports · 2025Article
- Structure Diversity and Properties of Some Bola-like Natural Products.Marine drugs · 2024Review
- 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
- The Unfinished Reconstructed Nature of the Last Universal Common Ancestor.Journal of molecular evolution · 2024Review
- Volatile Organic Compound Metabolism on Early Earth.Journal of molecular evolution · 2024Article
- Evolution of Cellular Organization Along the First Branches of the Tree of Life.Journal of molecular evolution · 2024Article
- 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
- Evolution of Intrinsic Disorder in Protein Loops.Life (Basel, Switzerland) · 2023Article
- A critical analysis of the current state of virus taxonomy.Frontiers in microbiology · 2023Review
- Protein folds as synapomorphies of the tree of life.Evolution; international journal of organic evolution · 2022Article
- A consensus view of the proteome of the last universal common ancestor.Ecology and evolution · 2022Article
- The Legend of ATP: From Origin of Life to Precision Medicine.Metabolites · 2022Review
- Scaling laws in enzyme function reveal a new kind of biochemical universality.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.