The rate and molecular spectrum of spontaneous mutations in the GC-rich multi-chromosome genome ofBurkholderia cenocepacia

Spontaneous mutations are ultimately essential for evolutionary change and are also the root cause of many diseases. However, until recently, both biological and technical barriers have prevented detailed analyses of mutation profiles, constraining our understanding of the mutation process to a few model organisms and leaving major gaps in our understanding of the role of genome content and structure on mutation. Here, we present a genome-wide view of the molecular mutation spectrum in Burkholderia cenocepacia, a clinically relevant pathogen with high %GC-content and multiple chromosomes. We find that B. cenocepacia has low genome-wide mutation rates with insertion-deletion mutations biased towards deletions, consistent with the idea that deletion pressure reduces prokaryotic genome sizes. Unlike prior studies of other organisms, mutations in B. cenocepacia are not AT-biased, which suggests that at least some genomes with high %GC-content experience unusual base-substitution mutation pressure. Importantly, we also observe variation in both the rates and spectra of mutations among chromosomes and elevated G:C>T:A transversions in late-replicating regions. Thus, although some patterns of mutation appear to be highly conserved across cellular life, others vary between species and even between chromosomes of the same species, potentially influencing the evolution of nucleotide composition and genome architecture.

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How do eubacterial organisms manage aggregation-prone proteome?

F1000Research ◽

10.12688/f1000research.4307.1 ◽

2014 ◽

Vol 3 ◽

pp. 137

Author(s):

Rishi Das Roy ◽

Manju Bhardwaj ◽

Vasudha Bhatnagar ◽

Kausik Chakraborty ◽

Debasis Dash

Keyword(s):

Protein Folding ◽

Genetic Material ◽

Gc Content ◽

Nucleotide Composition ◽

Population Bottlenecks ◽

Deleterious Mutations ◽

Aggregation Propensity ◽

Genome Wide ◽

A Genome ◽

Folding Simulations

Eubacterial genomes vary considerably in their nucleotide composition. The percentage of genetic material constituted by guanosine and cytosine (GC) nucleotides ranges from 20% to 70%. It has been posited that GC-poor organisms are more dependent on protein folding machinery. Previous studies have ascribed this to the accumulation of mildly deleterious mutations in these organisms due to population bottlenecks. This phenomenon has been supported by protein folding simulations, which showed that proteins encoded by GC-poor organisms are more prone to aggregation than proteins encoded by GC-rich organisms. To test this proposition using a genome-wide approach, we classified different eubacterial proteomes in terms of their aggregation propensity and chaperone-dependence using multiple machine learning models. In contrast to the expected decrease in protein aggregation with an increase in GC richness, we found that the aggregation propensity of proteomes increases with GC content. A similar and even more significant correlation was obtained with the GroEL-dependence of proteomes: GC-poor proteomes have evolved to be less dependent on GroEL than GC-rich proteomes. We thus propose that a decrease in eubacterial GC content may have been selected in organisms facing proteostasis problems.

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Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii

Genetics ◽

10.1534/genetics.120.303299 ◽

2020 ◽

Vol 215 (4) ◽

pp. 1107-1116 ◽

Cited By ~ 1

Author(s):

Sibel Kucukyildirim ◽

Megan Behringer ◽

Emily M. Williams ◽

Thomas G. Doak ◽

Michael Lynch

Keyword(s):

Molecular Mechanisms ◽

Model Organism ◽

Optimal Growth ◽

Haloferax Volcanii ◽

Base Substitution ◽

Spontaneous Mutations ◽

Evolutionary Forces ◽

Genome Wide ◽

Archaeal Species ◽

A Genome

Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth’s biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10−10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20–45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

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Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

Epigenetics & Chromatin ◽

10.1186/s13072-020-00361-9 ◽

2020 ◽

Vol 13 (1) ◽

Cited By ~ 1

Author(s):

Suhua Feng ◽

Zhenhui Zhong ◽

Ming Wang ◽

Steven E. Jacobsen

Keyword(s):

Dna Methylation ◽

Bisulfite Sequencing ◽

Accurate Determination ◽

Gc Content ◽

Epigenetic Mark ◽

Whole Genome ◽

Whole Genome Bisulfite Sequencing ◽

Genome Wide ◽

A Genome ◽

Genome Bisulfite Sequencing

Abstract Background 5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing. Results Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions. Conclusion We suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.

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A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0904895106 ◽

2009 ◽

Vol 106 (38) ◽

pp. 16310-16314 ◽

Cited By ~ 175

Author(s):

D. R. Denver ◽

P. C. Dolan ◽

L. J. Wilhelm ◽

W. Sung ◽

J. I. Lucas-Lledo ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Base Substitution ◽

Genome Wide ◽

A Genome ◽

Substitution Mutation

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Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in Vibrio cholerae and Vibrio fischeri

10.1101/066829 ◽

2016 ◽

Author(s):

Marcus M Dillon ◽

Way Sung ◽

Robert Sebra ◽

Michael Lynch ◽

Vaughn Cooper

Keyword(s):

Vibrio Cholerae ◽

Vibrio Fischeri ◽

Purifying Selection ◽

Base Substitution ◽

Chromosome 2 ◽

Spontaneous Mutations ◽

Wild Type ◽

Bacterial Genomes ◽

Genome Wide ◽

Mutation Spectra

The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae. Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-GC% squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. V. fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.

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Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

Frontiers in Genetics ◽

10.3389/fgene.2021.622724 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xuhao Song ◽

Tingbang Yang ◽

Xinyi Zhang ◽

Ying Yuan ◽

Xianghui Yan ◽

...

Keyword(s):

Genome Size ◽

Gc Content ◽

Distribution Patterns ◽

Functional Roles ◽

Tree Shrews ◽

Copy Numbers ◽

Genome Wide ◽

A Genome ◽

Dinucleotide Motif ◽

Evolution Of Mammals

Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

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Efficient genome-wide first-generation phenotypic screening system in mice using thepiggyBactransposon

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1906354116 ◽

2019 ◽

Vol 116 (37) ◽

pp. 18507-18516 ◽

Cited By ~ 3

Author(s):

Hao Chang ◽

Yukun Pan ◽

Sean Landrette ◽

Sheng Ding ◽

Dong Yang ◽

...

Keyword(s):

First Generation ◽

Cranial Nerves ◽

Model Organisms ◽

Biological Traits ◽

Screening System ◽

Loss Of Function ◽

Developmental Defects ◽

Genome Wide ◽

A Genome ◽

Milk Ingestion

Genome-wide phenotypic screens provide an unbiased way to identify genes involved in particular biological traits, and have been widely used in lower model organisms. However, cost and time have limited the utility of such screens to address biological and disease questions in mammals. Here we report a highly efficientpiggyBac(PB) transposon-based first-generation (F1) dominant screening system in mice that enables an individual investigator to conduct a genome-wide phenotypic screen within a year with fewer than 300 cages. ThePBscreening system uses visually trackable transposons to induce both gain- and loss-of-function mutations and generates genome-wide distributed new insertions in more than 55% of F1 progeny. Using this system, we successfully conducted a pilot F1 screen and identified 5 growth retardation mutations. One of these mutants, a Six1/4PB/+mutant, revealed a role in milk intake behavior. The mutant animals exhibit abnormalities in nipple recognition and milk ingestion, as well as developmental defects in cranial nerves V, IX, and X. ThisPBF1 screening system offers individual laboratories unprecedented opportunities to conduct affordable genome-wide phenotypic screens for deciphering the genetic basis of mammalian biology and disease pathogenesis.

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Switch in Codon Bias and Increased Rates of Amino Acid Substitution in the Drosophila saltans Species Group

Genetics ◽

10.1093/genetics/153.1.339 ◽

1999 ◽

Vol 153 (1) ◽

pp. 339-350 ◽

Cited By ~ 2

Author(s):

Francisco Rodríguez-Trelles ◽

Rosa Tarrío ◽

Francisco J Ayala

Keyword(s):

Rapid Evolution ◽

Gc Content ◽

Nucleotide Composition ◽

Species Group ◽

Effective Population ◽

Recombination Rates ◽

Mutation Pressure ◽

Saltans Group ◽

Codon Use ◽

Population Numbers

Abstract We investigated the nucleotide composition of five genes, Xdh, Adh, Sod, Per, and 28SrRNA, in nine species of Drosophila (subgenus Sophophora) and one of Scaptodrosophila. The six species of the Drosophila saltans group markedly differ from the others in GC content and codon use bias. The GC content in the third codon position, and to a lesser extent in the first position and the introns, is higher in the D. melanogaster and D. obscura groups than in the D. saltans group (in Scaptodrosophila it is intermediate but closer to the melanogaster and obscura species). Differences are greater for Xdh than for Adh, Sod, Per, and 28SrRNA, which are functionally more constrained. We infer that rapid evolution of GC content in the saltans lineage is largely due to a shift in mutation pressure, which may have been associated with diminished natural selection due to smaller effective population numbers rather than reduced recombination rates. The rate of GC content evolution impacts the rate of protein evolution and may distort phylogenetic inferences. Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated.

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Following the Trail of One Million Genomes: Footprints of SARS-CoV-2 Adaptation to Humans

10.1101/2021.05.07.443114 ◽

2021 ◽

Author(s):

Saymon Akther ◽

Edgaras Bezrucenkovas ◽

Li Li ◽

Brian Sulkow ◽

Lia Di ◽

...

Keyword(s):

Vaccine Development ◽

Immune Escape ◽

Local Level ◽

Genome Structure ◽

Base Substitution ◽

Human Populations ◽

Clonal Interference ◽

Adaptive Mutations ◽

Genome Wide ◽

A Genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has accumulated genomic mutations at an approximately linear rate since it first infected human populations in late 2019. Controversies remain regarding the identity, proportion, and effects of adaptive mutations as SARS-CoV-2 evolves from a bat- to a human-adapted virus. The potential for vaccine-escape mutations poses additional challenges in pandemic control. Despite being of great interest to therapeutic and vaccine development, human-adaptive mutations in SARS-CoV-2 are masked by a genome-wide linkage disequilibrium under which neutral and even deleterious mutations can reach fixation by chance or through hitchhiking. Furthermore, genome-wide linkage equilibrium imposes clonal interference by which multiple adaptive mutations compete against one another. Informed by insights from microbial experimental evolution, we analyzed close to one million SARS-CoV-2 genomes sequenced during the first year of the COVID-19 pandemic and identified putative human-adaptive mutations according to the rates of synonymous and missense mutations, temporal linkage, and mutation recurrence. Furthermore, we developed a forward-evolution simulator with the realistic SARS-CoV-2 genome structure and base substitution probabilities able to predict viral genome diversity under neutral, background selection, and adaptive evolutionary models. We conclude that adaptive mutations have emerged early, rapidly, and constantly to dominate SARS-CoV-2 populations despite clonal interference and purifying selection. Our analysis underscores a need for genomic surveillance of mutation trajectories at the local level for early detection of adaptive and immune-escape variants. Putative human-adaptive mutations are over-represented in viral proteins interfering host immunity and binding host-cell receptors and thus may serve as priority targets for designing therapeutics and vaccines against human-adapted forms of SARS-CoV-2.

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A genome-wide screen identifies genes that suppress the accumulation of spontaneous mutations in young and aged yeast cells

10.1101/492587 ◽

2018 ◽

Author(s):

Daniele Novarina ◽

Georges Janssens ◽

Koen Bokern ◽

Tim Schut ◽

Noor van Oerle ◽

...

Keyword(s):

Mutation Rate ◽

Genome Stability ◽

Genome Instability ◽

Spontaneous Mutation ◽

Yeast Cells ◽

Spontaneous Mutations ◽

Genome Maintenance ◽

Spontaneous Mutation Rate ◽

Genome Wide ◽

A Genome

To ensure proper transmission of genetic information, cells need to preserve and faithfully replicate their genome, and failure to do so leads to genome instability, a hallmark of both cancer and aging. Defects in genes involved in guarding genome stability cause several human progeroid syndromes, and an age-dependent accumulation of mutations has been observed in different organisms, from yeast to mammals. However, it is unclear if the spontaneous mutation rate changes during aging, and if specific pathways are important for genome maintenance in old cells. We developed a high-throughput replica-pinning approach to screen for genes important to suppress the accumulation of spontaneous mutations during yeast replicative aging. We found 13 known mutation suppression genes, and 31 genes that had no previous link to spontaneous mutagenesis, and all acted independently of age. Importantly, we identified PEX19, encoding an evolutionarily conserved peroxisome biogenesis factor, as an age-specific mutation suppression gene. While wild-type and pex19Δ young cells have similar spontaneous mutation rates, aged cells lacking PEX19 display an elevated mutation rate. This finding suggests that functional peroxisomes are important to preserve genome integrity specifically in old cells, possibly due to their role in reactive oxygen species metabolism.

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