Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea

Nishida, Hiromi

doi:10.21775/cimb.015.019

Cited by 12 publications

(1 citation statement)

References 78 publications

(69 reference statements)

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“…The GC content of a genome is the fraction of bases that are either guanine (G) or cytosine (C). It is a stable trait of a given prokaryotic genome, taking values from 16% to 77% (Nishida, 2013). Molecular mechanisms leading to both higher (Lassalle et al, 2015) and lower (Hershberg & Petrov, 2010) GC contents have been described.…”

Section: Introductionmentioning

confidence: 99%

r/K selection of GC content in prokaryotes

Aliperti,

Aptekmann,

Farfañuk

et al. 2023

Environmental Microbiology

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The guanine/cytosine (GC) content of prokaryotic genomes is species‐specific, taking values from 16% to 77%. This diversity of selection for GC content remains contentious. We analyse the correlations between GC content and a range of phenotypic and genotypic data in thousands of prokaryotes. GC content integrates well with these traits into r/K selection theory when phenotypic plasticity is considered. High GC‐content prokaryotes are r‐strategists with cheaper descendants thanks to a lower average amino acid metabolic cost, colonize unstable environments thanks to flagella and a bacillus form and are generalists in terms of resource opportunism and their defence mechanisms. Low GC content prokaryotes are K‐strategists specialized for stable environments that maintain homeostasis via a high‐cost outer cell membrane and endospore formation as a response to nutrient deprivation, and attain a higher nutrient‐to‐biomass yield. The lower proteome cost of high GC content prokaryotes is driven by the association between GC‐rich codons and cheaper amino acids in the genetic code, while the correlation between GC content and genome size may be partly due to functional diversity driven by r/K selection. In all, molecular diversity in the GC content of prokaryotes may be a consequence of ecological r/K selection.

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Section: Introductionmentioning

confidence: 99%

r/K selection of GC content in prokaryotes

Aliperti,

Aptekmann,

Farfañuk

et al. 2023

Environmental Microbiology

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Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae

Nishida

Katayama

Suzuki

et al. 2013

Gene

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Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers

Duan

Ding

Navarre

et al. 2021

Molecular Biology and Evolution

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Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly-acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from non-self DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range, and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.

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Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea

Cited by 12 publications

References 78 publications

r/K selection of GC content in prokaryotes

r/K selection of GC content in prokaryotes

Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae

Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers

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