ArticlePloS one2012
Phylogenomics of prokaryotic ribosomal proteins.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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Who cites it
152 citing papers in PubMed.
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- A family of ribosome hibernation factors widespread in Archaea.Nature communications · 2026Article
- Structure of a specialized 70S initiation complex.Nucleic acids research · 2026Article
- Multi-proteins similarity-based sampling to select representative genomes from large databases.BMC bioinformatics · 2025Article
- Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae.Nucleic acids research · 2025Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.Nature communications · 2025Article
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- Using Mycobacterium smegmatis as a Bioindicator for Zinc-limited Growth Conditions in Mycobacteria.Journal of visualized experiments : JoVE · 2024Article
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins.Nature microbiology · 2024Article
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- On the origin of the nucleus: a hypothesis.Microbiology and molecular biology reviews : MMBR · 2023Review
- Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales.Genome biology and evolution · 2023Article
- Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.Genome biology · 2023Article
- Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis.Microbiome · 2023Article
92 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies.
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