ArticleMolecular biology and evolution2012
Large variations in bacterial ribosomal RNA genes.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.Nucleic acids research · 2025Article
- The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics.Molecular biology and evolution · 2024Article
- Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.PloS one · 2024Article
- Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome.Nucleic acids research · 2022Article
- High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS.ISME communications · 2022Article
- Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis.RNA (New York, N.Y.) · 2022Article
- A high-quality reference genome for the fish pathogenMicrobial genomics · 2022Article
- Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.Nucleic acids research · 2021Article
- Simplification of Ribosomes in Bacteria with Tiny Genomes.Molecular biology and evolution · 2021Article
- Article
- Antimicrobial susceptibility and genetic profile of Mycoplasma hyopneumoniae isolates from Brazil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2020Article
- Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria.Nucleic acids research · 2019Article
- Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Genome research · 2018Article
- Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands.Molecular biology and evolution · 2018Article
- Re-annotation of 12,495 prokaryotic 16S rRNA 3' ends and analysis of Shine-Dalgarno and anti-Shine-Dalgarno sequences.PloS one · 2018Article
- Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs.PloS one · 2018Article
- Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.Scientific reports · 2017Article
- Flipping chromosomes in deep-sea archaea.PLoS genetics · 2017Article
- How Changes in Anti-SD Sequences Would Affect SD Sequences inG3 (Bethesda, Md.) · 2017Article
- Comparative Genomics of Host-Symbiont and Free-Living Oceanobacillus Species.Genome biology and evolution · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosomal RNA (rRNA) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. Here, we explored large-scale variations of rRNA genes through bioinformatic analyses of available complete bacterial genomic sequences with an emphasis on formation mechanisms and biological significance. Interestingly, we found bacterial genomes in which no 16S rRNA genes harbor the conserved core of the anti-Shine-Dalgarno sequence (5'-CCTCC-3'). This loss was accompanied by elimination of Shine-Dalgarno-like sequences upstream of their protein-coding genes. Those genomes belong to 1 or 2 of the following categories: primary symbionts, hemotropic Mycoplasma, and Flavobacteria. We also found many rearranged rRNA genes and reconstructed their history. Conjecturing the underlying mechanisms, such as inversion, partial duplication, transposon insertion, deletion, and substitution, we were able to infer their biological significance, such as co-orientation of rRNA transcription and chromosomal replication, lateral transfer of rRNA gene segments, and spread of rRNA genes with an apparent structural defect through gene conversion. These results open the way to understanding dynamic evolutionary changes of rRNA genes and the translational machinery.
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