Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

ABSTRACT The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (F opt ) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between F opt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, “high-status” genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.

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Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans

Microorganisms ◽

10.3390/microorganisms8060900 ◽

2020 ◽

Vol 8 (6) ◽

pp. 900

Author(s):

Gema Carrasco ◽

Sara Monzón ◽

María San Segundo ◽

Enrique García ◽

Noelia Garrido ◽

...

Keyword(s):

16S Rrna ◽

Topoisomerase Ii ◽

Gc Content ◽

Amino Acid Identity ◽

Beta Lactams ◽

Nocardia Species ◽

Antimicrobial Susceptibilities ◽

The Difference ◽

Subunit B ◽

Genomic Gc Content

Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).

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Role of GC-biased mutation pressure on synonymous codon choice inMicrococcus luteusa bacterium with a high genomic GC-content

Nucleic Acids Research ◽

10.1093/nar/18.6.1565 ◽

1990 ◽

Vol 18 (6) ◽

pp. 1565-1569 ◽

Cited By ~ 51

Author(s):

Takeshi Ohama ◽

Akira Muto ◽

Syozo Osawa

Keyword(s):

Synonymous Codon ◽

Gc Content ◽

Mutation Pressure ◽

Genomic Gc Content

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Genome size and genomic GC content evolution in the miniature genome-sized family Lentibulariaceae

New Phytologist ◽

10.1111/nph.12790 ◽

2014 ◽

Vol 203 (1) ◽

pp. 22-28 ◽

Cited By ~ 33

Author(s):

Adam Veleba ◽

Petr Bureš ◽

Lubomír Adamec ◽

Petr Šmarda ◽

Ivana Lipnerová ◽

...

Keyword(s):

Genome Size ◽

Gc Content ◽

Genomic Gc Content

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Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences

Annals of Botany ◽

10.1093/aob/mcaa133 ◽

2020 ◽

Vol 126 (6) ◽

pp. 1077-1087

Author(s):

Dora Čertnerová ◽

Pavel Škaloud

Keyword(s):

Growth Rate ◽

Genome Size ◽

Cell Size ◽

Nuclear Dna ◽

Gc Content ◽

Size Variation ◽

Nuclear Dna Content ◽

Genome Size Variation ◽

Adaptive Consequences ◽

Genomic Gc Content

Abstract Background and Aims While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. Methods Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. Key Results Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. Conclusions Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

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Genomic GC-Content Affects the Accuracy of 16S rRNA Gene Sequencing Based Microbial Profiling due to PCR Bias

Frontiers in Microbiology ◽

10.3389/fmicb.2017.01934 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 25

Author(s):

Martin F. Laursen ◽

Marlene D. Dalgaard ◽

Martin I. Bahl

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gc Content ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Pcr Bias ◽

Microbial Profiling ◽

Rrna Gene Sequencing ◽

Genomic Gc Content

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Variations in amino acid composition in bacterial single stranded DNA–binding proteins correlate with GC content

Periodicum Biologorum ◽

10.18054/pb.v118i4.4847 ◽

2017 ◽

Vol 118 (4) ◽

Cited By ~ 1

Author(s):

Tina Paradžik ◽

Želimira Filić ◽

Dušica Vujaklija

Keyword(s):

Amino Acid ◽

Gc Content ◽

16S Rrna Genes ◽

Rrna Genes ◽

Significant Drop ◽

Bacterial Phyla ◽

Terminal Domain ◽

Wide Range ◽

Ssb Proteins ◽

Genomic Gc Content

Background and purposeSSB proteins are essential for the maintenance of the genome in all domains of life. Most bacterial SSBs are active as homotetramers. Each monomer comprises N-terminal domain (OB-fold) which is responsible for ssDNA binding and a disordered C-terminal domain (Ct) with a conserved acidic tail responsible for protein interactions.The variations in these essential proteins prompted us to conduct in silico analyses of the aa composition and properties of two distinct SSB domains in relation to bacterial GC content.Materials and methodsSSB sequences were collected from genomes covering a wide range of GC content from 14 bacterial phyla. The maximum-likelihood (ML) trees were constructed for SSB sequences and corresponding 16S rRNA genes. The aa contents of OB folds and Ct domains were subsequently analysed. ResultsWe showed that SSB proteins followed predicted amino acid (aa) composition as a function of genomic GC content. However, two distinct domains of SSB exhibit significant differences to the expected aa composition. Variations in aa proportion were more prominent in Ct domains. Elevated accumulation of Gly (up to 60 %) and Pro (up to 24 %), significant drop in the proportion of basic Lys and reduction in hydrophobic Leu, Ile and Val were identified in Ct domains of SSBs from high GC genomes. Consequently, this influences the biochemical properties of Ct domains.ConclusionsBased on this comparative study of SSBs we conclude that genomic GC content and two distinct domains with different functional roles participate in shaping aa composition of SSB proteins.

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Potential link between selection for high GC content and repair of double strand breaks in prokaryotic genomes

10.1101/544924 ◽

2019 ◽

Author(s):

Jake L. Weissman ◽

William F. Fagan ◽

Philip L.F. Johnson

Keyword(s):

Gc Content ◽

Preliminary Evidence ◽

Selective Adaptation ◽

Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Novel Association ◽

Selection For ◽

Non Homologous End Joining ◽

Genomic Gc Content

AbstractGenomic GC content varies widely among microbes for reasons unknown. While mutation bias partially explains this variation, prokaryotes near-universally have a higher GC content than predicted solely by this bias. Debate surrounds the relative importance of the remaining explanations of selection versus biased gene conversion favoring GC alleles. Some environments (e.g. soils) are associated with a high genomic GC content of their inhabitants, which implies that this content may be a selective adaptation to particular habitats. Here, we report a novel association between the presence of the non-homologous end joining DNA doublestrand break repair pathway and GC content; this observation suggests that high GC content may be an adaptation to facilitate repair of double strand breaks when homologous recombination is not possible. We discuss potential mechanisms accounting for the observed association, and provide preliminary evidence that sites experiencing higher rates of doublestrand breaks are under selection for increased GC content relative to the genomic background.

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