ArticleBMC evolutionary biology2009
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 23 citations in OpenAlex.
- Review
- Gliotoxin and related metabolites as zinc chelators: implications and exploitation to overcome antimicrobial resistance.Essays in biochemistry · 2023Article
- Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA.Nucleic acids research · 2023Article
- Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates.PloS one · 2021Article
- Occurrence of randomly recombined functional 16S rRNA genes in Thermus thermophilus suggests genetic interoperability and promiscuity of bacterial 16S rRNAs.Scientific reports · 2019Article
- Comparative RNA function analysis reveals high functional similarity between distantly related bacterial 16 S rRNAs.Scientific reports · 2017Article
- The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles.BMC genomics · 2014Article
- Specific contacts between protein S4 and ribosomal RNA are required at multiple stages of ribosome assembly.RNA (New York, N.Y.) · 2013Article
- Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations.The journal of physical chemistry. B · 2012Article
- Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.Advances in microbial physiology · 2012Review
- Phylogenomics of prokaryotic ribosomal proteins.PloS one · 2012Article
- Slow formation of stable complexes during coincubation of minimal rRNA and ribosomal protein S4.Journal of molecular biology · 2011Article
- Telling the whole story in a 10,000-genome world.Biology direct · 2011Article
- Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.PloS one · 2011Article
- Functional role of ribosomal signatures.Biophysical journal · 2010Article
- Translational selection is ubiquitous in prokaryotes.PLoS genetics · 2010Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe universal ribosomal protein S4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. Being part of the information processing machinery of the cell, the gene for S4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. Here we report the evolution of ribosomal protein S4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution.
resultsIn this study we present the complex evolutionary history of ribosomal protein S4 using 660 bacterial genomes from 16 major bacterial phyla. According to conserved characteristics in the sequences, S4 can be classified into C+ (zinc-binding) and C- (zinc-free) variants, with 26 genomes (mainly from the class Clostridia) containing genes for both. A maximum likelihood phylogenetic tree of the S4 sequences was incongruent with the standard bacterial phylogeny, indicating a departure from strict vertical inheritance. Further analysis using the genome content near the S4 genes, which are usually located in a conserved gene cluster, showed not only that HGT of the C- gene had occurred at various stages of bacterial evolution, but also that both the C- and C+ genes were present before the individual phyla diverged. To explain the latter, we theorize that a gene pool existed early in bacterial evolution from which bacteria could sample S4 gene variants, according to environmental conditions. The distribution of the C+/- variants for seven other zinc-binding ribosomal proteins in these 660 bacterial genomes is consistent with that seen for S4 and may shed light on the evolutionary pressures involved.
conclusionThe complex history presented for "core" protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects the pervasive nature of HGT in subsequent bacterial evolution. This has implications for both theoretical models of evolution and practical applications of phylogenetic reconstruction as well as the control of zinc economy in bacterial cells.
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