Positive correlations between genomic %<scp>AT</scp> and genome size within strains of bacterial species

Bohlin, Jon; Sekse, Camilla; Skjerve, Eystein; Brynildsrud, Ola Brønstad

doi:10.1111/1758-2229.12145

Cited by 22 publications

(25 citation statements)

References 30 publications

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“…Indeed, we found a negative correlation between the genome size and the GC content for the Legionella genomes, which also suggests frequent HGT ( Fig. 1D) (19). Despite the importance of flagella for transmission to new hosts, as shown for L. pneumophila, flagella encoding genes were not conserved in all species but showed a patchy distribution, as 23 of the 80 strains analyzed lacked flagella genes (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 70%

More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

Gómez-Valero

Rusniok

Carson

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

189

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The genusLegionellacomprises 65 species, among whichLegionella pneumophilais a human pathogen causing severe pneumonia. To understand the evolution of an environmental to an accidental human pathogen, we have functionally analyzed 80Legionellagenomes spanning 58 species. Uniquely, an immense repository of 18,000 secreted proteins encoding 137 different eukaryotic-like domains and over 200 eukaryotic-like proteins is paired with a highly conserved type IV secretion system (T4SS). Specifically, we show that eukaryotic Rho- and Rab-GTPase domains are found nearly exclusively in eukaryotes andLegionella. Translocation assays for selected Rab-GTPase proteins revealed that they are indeed T4SS secreted substrates. Furthermore, F-box, U-box, and SET domains were present in >70% of all species, suggesting that manipulation of host signal transduction, protein turnover, and chromatin modification pathways are fundamental intracellular replication strategies for legionellae. In contrast, the Sec-7 domain was restricted toL. pneumophilaand seven other species, indicating effector repertoire tailoring within different amoebae. Functional screening of 47 species revealed 60% were competent for intracellular replication in THP-1 cells, but interestingly, this phenotype was associated with diverse effector assemblages. These data, combined with evolutionary analysis, indicate that the capacity to infect eukaryotic cells has been acquired independently many times within the genus and that a highly conserved yet versatile T4SS secretes an exceptional number of different proteins shaped by interdomain gene transfer. Furthermore, we revealed the surprising extent to which legionellae have coopted genes and thus cellular functions from their eukaryotic hosts, providing an understanding of how dynamic reshuffling and gene acquisition have led to the emergence of major human pathogens.

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Section: Resultsmentioning

confidence: 70%

More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

Gómez-Valero

Rusniok

Carson

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

189

274

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“…The recent development of high-throughput sequencing technology has reduced sequencing costs and for many microbial species there are now multiple strains, completely sequenced and assembled, available for analyses in public databases [ 10 ]. This allowed us to explore strain-level relationships between base composition, genome size and predicted HGT in several microbial species in a recent study [ 11 ]. We found that the genome size, compared at strain-level, was predominantly correlated with genomic AT content, contrary to what has been found for prokaryotes in general [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…We found that the genome size, compared at strain-level, was predominantly correlated with genomic AT content, contrary to what has been found for prokaryotes in general [ 12 ]. Additionally, AT content correlated with predicted HGT size, which again correlated with chromosome size [ 11 ]. In this study we also analyzed the influence of selective pressures on microbial genome size using the concept of relative entropy [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli

et al. 2014

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BackgroundThere are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation.ResultsHierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (p<0.001). This is further supported by a linear association between strain-wise dS and dN values (β = 26.94 ± 0.44, R2~0.98, p<0.001). The non-core part of the genome was also significantly more AT-rich (p<0.001) than the core genome and E. coli genome size correlated with estimated HGT size (p<0.001). In addition, genome size (p<0.001), AT content (p<0.001) as well as estimated HGT size (p<0.005) were all associated with the presence of virulence factors, suggesting that pathogenicity traits in E. coli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98).ConclusionsOn a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-882) contains supplementary material, which is available to authorized users.

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“…The red distribution represents GC→ AT mutation rates while the blue distribution AT→ GC mutation rates corresponding estimated distributions for β. A notable exception is the case of the pathogen Francisella tularensis, which is known for its ability to acquire DNA horizontally [16]. Additionally, only 12 closed strains of F. tularensis were available, so genomic heterogeneity between its strains might bias estimates.…”

Section: Resultsmentioning

confidence: 99%

Estimation of AT and GC content distributions of nucleotide substitution rates in bacterial core genomes

2019

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Background: Genomic GC content varies both within and, substantially, between microbial genomes. While some of this variation can be explained by evolutionary divergence and environmental factors, a notable portion is not understood. To investigate further, we explore a non-linear mathematical model (gcMOD) of singlenucleotide polymorphism (SNP) GC content (sbGC, the GC content of substituted bases) as a function of core genome GC content (cgGC). We estimate the model's parameters using Bayesian inference on empirical genetic data from the microbial core genomes of 35 bacterial species, each of which contains at least 10 representative strains. We utilize 716 bacterial genomes in total. We also explore some possible implications that result from the mathematical properties of gcMOD. Results: We find that the median GC → AT substitution rates (β) are almost always considerably higher than the corresponding AT → GC substitution rates (α) for all 35 core genomes. The distribution of β is also noticeably more concentrated (i.e. thinner) than the corresponding distribution of α for almost all species, excepting the bacteria with the most GC-rich genomes. We also demonstrate that at the singularity point of gcMOD (where α = β), the model is reduced to a linear equation. By analyzing the linear model, we show that due to the constraints on gcMOD, the mutation rates can have profound influence on both cgGC as well as sbGC. Moreover, by examining the mathematical properties of gcMOD's inverse function, we find that change in cgGC, and hence in genomic GC content, can potentially occur quite rapidly. Conclusions: Examining the distributions of the GC → AT and AT → GC substitution rates for 35 bacterial species, we demonstrate that the former (β) are remarkably similar for all species examined. In addition, GC → AT substitution rate distributions were considerably more concentrated for all species, with the mode consistently peaking at higher rates than for AT → GC substitution rates.

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Positive correlations between genomic %AT and genome size within strains of bacterial species

Cited by 22 publications

References 30 publications

More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli

Estimation of AT and GC content distributions of nucleotide substitution rates in bacterial core genomes

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