Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection

Steinrueck, Magdalena; Guet, Călin C.

doi:10.7554/elife.25100

Cited by 19 publications

(32 citation statements)

References 70 publications

(117 reference statements)

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“…High rates of mutation caused by insertion and removal of either short duplications or IS elements can thus play an important role in the ecology and evolution of bacteria. Recent experiments also support this perspective [ 34 , 64 ].…”

Section: Discussionmentioning

confidence: 75%

Leaky resistance and the conditions for the existence of lytic bacteriophage

et al. 2018

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In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIR is maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIR in these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”

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Section: Discussionmentioning

confidence: 75%

Leaky resistance and the conditions for the existence of lytic bacteriophage

et al. 2018

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“…We sought to construct a reporter for CNVs that occur at a given locus of interest. Based on previous studies [53–56], we hypothesized that CNVs that alter the number of copies of a constitutively expressed fluorescent protein gene would facilitate single-cell detection of de novo copy number variation. To test the feasibility of this approach, we constructed haploid S .…”

Section: Resultsmentioning

confidence: 99%

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

et al. 2018

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Copy number variants (CNVs) are a pervasive source of genetic variation and evolutionary potential, but the dynamics and diversity of CNVs within evolving populations remain unclear. Long-term evolution experiments in chemostats provide an ideal system for studying the molecular processes underlying CNV formation and the temporal dynamics with which they are generated, selected, and maintained. Here, we developed a fluorescent CNV reporter to detect de novo gene amplifications and deletions in individual cells. We used the CNV reporter in Saccharomyces cerevisiae to study CNV formation at the GAP1 locus, which encodes the general amino acid permease, in different nutrient-limited chemostat conditions. We find that under strong selection, GAP1 CNVs are repeatedly generated and selected during the early stages of adaptive evolution, resulting in predictable dynamics. Molecular characterization of CNV-containing lineages shows that the CNV reporter detects different classes of CNVs, including aneuploidies, nonreciprocal translocations, tandem duplications, and complex CNVs. Despite GAP1’s proximity to repeat sequences that facilitate intrachromosomal recombination, breakpoint analysis revealed that short inverted repeat sequences mediate formation of at least 50% of GAP1 CNVs. Inverted repeat sequences are also found at breakpoints at the DUR3 locus, where CNVs are selected in urea-limited chemostats. Analysis of 28 CNV breakpoints indicates that inverted repeats are typically 8 nucleotides in length and separated by 40 bases. The features of these CNVs are consistent with origin-dependent inverted-repeat amplification (ODIRA), suggesting that replication-based mechanisms of CNV formation may be a common source of gene amplification. We combined the CNV reporter with barcode lineage tracking and found that 102–104 independent CNV-containing lineages initially compete within populations, resulting in extreme clonal interference. However, only a small number (18–21) of CNV lineages ever constitute more than 1% of the CNV subpopulation, and as selection progresses, the diversity of CNV lineages declines. Our study introduces a novel means of studying CNVs in heterogeneous cell populations and provides insight into their dynamics, diversity, and formation mechanisms in the context of adaptive evolution.

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“…Based on previous studies [53][54][55][56] , we hypothesized that CNVs that alter the number of copies of a constitutively expressed fluorescent protein gene would facilitate single cell detection of de novo copy number variation. To test the feasibility of this approach, we constructed haploid Saccharomyces cerevisiae strains isogenic to the reference strain (S288c) with one or two copies of a constitutively expressed GFP variant, mCitrine [57] , and diploid strains with 1-4 copies of mCitrine integrated into the genome ( Table S1 ).…”

Section: Resultsmentioning

confidence: 99%

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

Lauer

Avecilla

Spealman

et al. 2018

Preprint

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Copy number variants (CNVs) are a pervasive, but understudied source of genetic variation and evolutionary potential. Long-term evolution experiments in chemostats provide an ideal system for studying the molecular processes underlying CNV formation and the temporal dynamics of de novo CNVs. Here, we developed a fluorescent reporter to monitor gene amplifications and deletions at a specific locus with single-cell resolution. Using a CNV reporter in nitrogen-limited chemostats, we find that GAP1 CNVs are repeatedly generated and selected during the early stages of adaptive evolution resulting in predictable dynamics of CNV selection. However, subsequent diversification of populations defines a second phase of evolutionary dynamics that cannot be predicted. Using whole genome sequencing, we identified a variety of GAP1 CNVs that vary in size and copy number. Despite GAP1 's proximity to tandem repeats that facilitate intrachromosomal recombination, we find that non-allelic homologous recombination (NAHR) between flanking tandem repeats occurs infrequently. Rather, breakpoint characterization revealed that for at least 50% of GAP1 CNVs, origin-dependent inverted-repeat amplification (ODIRA), a DNA replication mediated process, is the likely mechanism. We also find evidence that ODIRA generates DUR3 CNVs, indicating that it may be a common mechanism of gene amplification. We combined the CNV reporter with barcode lineage tracking and found that 10 3 -10 4 independent CNV-containing lineages initially compete within populations, which results in extreme clonal interference. Our study introduces a novel means of studying CNVs in heterogeneous cell populations and provides insight into the underlying dynamics of CNVs in evolution.condition [32,33] . A high rate of CNV formation suggests that multiple, independent CNV-containing lineages may compete during adaptive evolution resulting in clonal interference, which is characteristic of large, evolving populations [29,[34][35][36] . However, the extent of clonal interference among CNV-containing lineages is unknown.The general amino acid permease, GAP1 , is ideally suited to studying the role of CNVs in adaptive evolution. GAP1 encodes a high-affinity transporter for all naturally occurring amino acids and analogues, and it is highly expressed in nitrogen-poor conditions [37,38] . We have previously shown that two classes of CNVs are selected at the GAP1 locus in S. cerevisiae : amplification alleles in glutamine and glutamate-limited chemostats and deletion alleles in ureaand allantoin-limited chemostats [24,25] . GAP1 CNVs are also found in natural populations.Multiple, tandem copies of GAP1 have been identified in wild populations of the nectar yeast, Metschnikowia reukaufii , which result in a competitive advantage over other microbes when amino acids are scarce [39] . As a frequent target of selection in adverse environments in both experimental and natural populations, GAP1 is a model locus for studying the dynamics and mechanisms underlying both gene amplification a...

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Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection

Cited by 19 publications

References 70 publications

Leaky resistance and the conditions for the existence of lytic bacteriophage

Leaky resistance and the conditions for the existence of lytic bacteriophage

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

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