ArticleJournal of bacteriology2021
Non-essential ribosomal proteins in bacteria and archaea identified using COGs.
Article in Journal of bacteriology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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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.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
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- Ribosomal allostery as a potential regulator of bacterial dormancy.Nature communications · 2026Article
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- Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.Applied and environmental microbiology · 2026Article
- Artificial Neural Network Elucidates the Role of Transport Proteins inMetabolites · 2026Article
- Screening a library of temperature-sensitive mutants to identify secretion factors inJournal of bacteriology · 2025Article
- Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.Nature communications · 2025Article
- Genomic personalities ofISME communications · 2025Article
- Uncovering newMicrobiology spectrum · 2024Article
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes.Genome biology · 2024Article
- How do bacterial endosymbionts work with so few genes?PLoS biology · 2024Article
- Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023.International journal of molecular sciences · 2024Review
- Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.ISME communications · 2024Article
- Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.Genome biology · 2023Article
- Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure.Computational and structural biotechnology journal · 2023Review
- A Ribosomal Protein Homolog Governs Gene Expression and Virulence in a Bacterial Pathogen.Journal of bacteriology · 2022Article
- A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle.Microbiome · 2022Article
- A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes.iScience · 2022Article
- Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis.RNA (New York, N.Y.) · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.
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.