ArticleJournal of molecular evolution2009
The evolutionary history of the structure of 5S ribosomal RNA.
Article in Journal of molecular evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 57 citations in OpenAlex.
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A robust machine learning model based on ribosomal-subunit-derived piRNAs for diagnostic potential of nonsmall cell lung cancer across multicentre, large-scale of sequencing data.Clinical and translational medicine · 2025Article
- Impacts of ribosomal RNA sequence variation on gene expression and phenotype.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Limitations of sequence dissimilarity as a predictor of prokaryotic lineage.Open biology · 2025Review
- Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae).The Plant journal : for cell and molecular biology · 2024Article
- Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling.International journal of molecular sciences · 2023Article
- Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis.RNA (New York, N.Y.) · 2022Article
- 5S Ribosomal DNA of GenusFrontiers in plant science · 2022Article
- Menzerath-Altmann's Law of Syntax in RNA Accretion History.Life (Basel, Switzerland) · 2021Article
- Expansion segments in bacterial and archaeal 5S ribosomal RNAs.RNA (New York, N.Y.) · 2021Article
- Descent of Bacteria and Eukarya From an Archaeal Root of Life.Evolutionary bioinformatics online · 2020Article
- Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.Evolutionary bioinformatics online · 2019Review
- Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification.Science progress · 2018Review
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
- Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life.Life (Basel, Switzerland) · 2016Article
- Molecular organization of the 5S rDNA gene type II in elasmobranchs.RNA biology · 2016Article
- Ancestral Insertions and Expansions of rRNA do not Support an Origin of the Ribosome in Its Peptidyl Transferase Center.Journal of molecular evolution · 2015Article
- Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology.Computational and structural biotechnology journal · 2015Review
- A tree of cellular life inferred from a genomic census of molecular functions.Journal of molecular evolution · 2014Article
- A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life.Archaea (Vancouver, B.C.) · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
5S rRNA is the smallest nucleic acid component of the large ribosomal subunit, contributing to ribosomal assembly, stability, and function. Despite being a model for the study of RNA structure and RNA-protein interactions, the evolution of this universally conserved molecule remains unclear. Here, we explore the history of the three-domain structure of 5S rRNA using phylogenetic trees that are reconstructed directly from molecular structure. A total of 46 structural characters describing the geometry of 666 5S rRNAs were used to derive intrinsically rooted trees of molecules and molecular substructures. Trees of molecules revealed the tripartite nature of life. In these trees, superkingdom Archaea formed a paraphyletic basal group, while Bacteria and Eukarya were monophyletic and derived. Trees of molecular substructures supported an origin of the molecule in a segment that is homologous to helix I (alpha domain), its initial enhancement with helix III (beta domain), and the early formation of the three-domain structure typical of modern 5S rRNA in Archaea. The delayed formation of the branched structure in Bacteria and Eukarya lends further support to the archaeal rooting of the tree of life. Remarkably, the evolution of molecular interactions between 5S rRNA and associated ribosomal proteins inferred from a census of domain structure in hundreds of genomes established a tight relationship between the age of 5S rRNA helices and the age of ribosomal proteins. Results suggest 5S rRNA originated relatively quickly but quite late in evolution, at a time when primordial metabolic enzymes and translation machinery were already in place. The molecule therefore represents a late evolutionary addition to the ribosomal ensemble that occurred prior to the early diversification of Archaea.
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