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González-González A, Batarseh TN, Rodríguez-Verdugo A, Gaut BS. Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the rho and rpoB Genes of Escherichia coli during High-Temperature Adaptation. Mol Biol Evol 2024; 41:msae187. [PMID: 39235107 DOI: 10.1093/molbev/msae187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Epistasis is caused by genetic interactions among mutations that affect fitness. To characterize properties and potential mechanisms of epistasis, we engineered eight double mutants that combined mutations from the rho and rpoB genes of Escherichia coli. The two genes encode essential functions for transcription, and the mutations in each gene were chosen because they were beneficial for adaptation to thermal stress (42.2 °C). The double mutants exhibited patterns of fitness epistasis that included diminishing returns epistasis at 42.2 °C, stronger diminishing returns between mutations with larger beneficial effects and both negative and positive (sign) epistasis across environments (20.0 °C and 37.0 °C). By assessing gene expression between single and double mutants, we detected hundreds of genes with gene expression epistasis. Previous work postulated that highly connected hub genes in coexpression networks have low epistasis, but we found the opposite: hub genes had high epistasis values in both coexpression and protein-protein interaction networks. We hypothesized that elevated epistasis in hub genes reflected that they were enriched for targets of Rho termination but that was not the case. Altogether, gene expression and coexpression analyses revealed that thermal adaptation occurred in modules, through modulation of ribonucleotide biosynthetic processes and ribosome assembly, the attenuation of expression in genes related to heat shock and stress responses, and with an overall trend toward restoring gene expression toward the unstressed state.
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Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Tiffany N Batarseh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
| | | | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
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2
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Chavhan Y, Malusare S, Dey S. Population size shapes trade-off dilution and adaptation to a marginal niche unconstrained by sympatric habitual conditions. Evolution 2024; 78:342-354. [PMID: 38038256 DOI: 10.1093/evolut/qpad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 11/06/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
How does niche expansion occur when the habitual (high-productivity) and marginal (low-productivity) niches are simultaneously available? Without spatial structuring, such conditions should impose fitness maintenance in the former while adapting to the latter. Hence, adaptation to a given marginal niche should be influenced by the identity of the simultaneously available habitual niche. This hypothesis remains untested. Similarly, it is unknown if larger populations, which can access greater variation and undergo more efficient selection, are generally better at niche expansion. We tested these hypotheses using a large-scale evolution experiment with Escherichia coli. While we observed widespread niche expansion, larger populations consistently adapted to a greater extent to both marginal and habitual niches. Owing to diverse selection pressures in different habitual niches (constant vs. fluctuating environments; environmental fluctuations varying in both predictability and speed), fitness in habitual niches was significantly shaped by their identities. Surprisingly, despite this diversity in habitual selection pressures, adaptation to the marginal niche was unconstrained by the habitual niche's identity. We show that in terms of fitness, two negatively correlated habitual niches can still have positive correlations with the marginal niche. This allows the marginal niche to dilute fitness trade-offs across habitual niches, thereby allowing costless niche expansion. Our results provide fundamental insights into the sympatric niche expansion.
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Affiliation(s)
- Yashraj Chavhan
- Biology Division, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sarthak Malusare
- Biology Division, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sutirth Dey
- Biology Division, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
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3
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Adaptation to Overflow Metabolism by Mutations That Impair tRNA Modification in Experimentally Evolved Bacteria. mBio 2023; 14:e0028723. [PMID: 36853041 PMCID: PMC10128029 DOI: 10.1128/mbio.00287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
When microbes grow in foreign nutritional environments, selection may enrich mutations in unexpected pathways connecting growth and homeostasis. An evolution experiment designed to identify beneficial mutations in Burkholderia cenocepacia captured six independent nonsynonymous substitutions in the essential gene tilS, which modifies tRNAIle2 by adding a lysine to the anticodon for faithful AUA recognition. Further, five additional mutants acquired mutations in tRNAIle2, which strongly suggests that disrupting the TilS-tRNAIle2 interaction was subject to strong positive selection. Mutated TilS incurred greatly reduced enzymatic function but retained capacity for tRNAIle2 binding. However, both mutant sets outcompeted the wild type by decreasing the lag phase duration by ~3.5 h. We hypothesized that lysine demand could underlie fitness in the experimental conditions. As predicted, supplemental lysine complemented the ancestral fitness deficit, but so did the additions of several other amino acids. Mutant fitness advantages were also specific to rapid growth on galactose using oxidative overflow metabolism that generates redox imbalance, not resources favoring more balanced metabolism. Remarkably, 13 tilS mutations also evolved in the long-term evolution experiment with Escherichia coli, including four fixed mutations. These results suggest that TilS or unknown binding partners contribute to improved growth under conditions of rapid sugar oxidation at the predicted expense of translational accuracy. IMPORTANCE There is growing evidence that the fundamental components of protein translation can play multiple roles in maintaining cellular homeostasis. Enzymes that interact with transfer RNAs not only ensure faithful decoding of the genetic code but also help signal the metabolic state by reacting to imbalances in essential building blocks like free amino acids and cofactors. Here, we present evidence of a secondary function for the essential enzyme TilS, whose only prior known function is to modify tRNAIle(CAU) to ensure accurate translation. Multiple nonsynonymous substitutions in tilS, as well as its cognate tRNA, were selected in evolution experiments favoring rapid, redox-imbalanced growth. These mutations alone decreased lag phase and created a competitive advantage, but at the expense of most primary enzyme function. These results imply that TilS interacts with other factors related to the timing of exponential growth and that tRNA-modifying enzymes may serve multiple roles in monitoring metabolic health.
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4
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Rana A, Patton D, Turner NT, Dillon MM, Cooper VS, Sung W. Precise measurement of the fitness effects of spontaneous mutations by droplet digital PCR in Burkholderia cenocepacia. Genetics 2021; 219:6325026. [PMID: 34849876 DOI: 10.1093/genetics/iyab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/12/2022] Open
Abstract
Understanding how mutations affect survivability is a key component to knowing how organisms and complex traits evolve. However, most mutations have a minor effect on fitness and these effects are difficult to resolve using traditional molecular techniques. Therefore, there is a dire need for more accurate and precise fitness measurements methods. Here, we measured the fitness effects in Burkholderia cenocepacia HI2424 mutation accumulation (MA) lines using droplet-digital polymerase chain reaction (ddPCR). Overall, the fitness measurements from ddPCR-MA are correlated positively with fitness measurements derived from traditional phenotypic marker assays (r = 0.297, P = 0.05), but showed some differences. First, ddPCR had significantly lower measurement variance in fitness (F = 3.78, P < 2.6 × 10-13) in control experiments. Second, the mean fitness from ddPCR-MA measurements were significantly lower than phenotypic marker assays (-0.0041 vs -0.0071, P = 0.006). Consistent with phenotypic marker assays, ddPCR-MA measurements observed multiple (27/43) lineages that significantly deviated from mean fitness, suggesting that a majority of the mutations are neutral or slightly deleterious and intermixed with a few mutations that have extremely large effects. Of these mutations, we found a significant excess of mutations within DNA excinuclease and Lys R transcriptional regulators that have extreme deleterious and beneficial effects, indicating that modifications to transcription and replication may have a strong effect on organismal fitness. This study demonstrates the power of ddPCR as a ubiquitous method for high-throughput fitness measurements in both DNA- and RNA-based organisms regardless of cell type or physiology.
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Affiliation(s)
- Anita Rana
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - David Patton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Nathan T Turner
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Marcus M Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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5
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Bakerlee CW, Phillips AM, Nguyen Ba AN, Desai MM. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations. eLife 2021; 10:e70918. [PMID: 34596043 PMCID: PMC8579951 DOI: 10.7554/elife.70918] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in each of three environments, and then assayed their fitness in multiple environments over 1000 generations of evolution. We find that replicate populations evolved in the same condition share common patterns of pleiotropic effects across other environments, which emerge within the first several hundred generations of evolution. However, we also find dynamic and environment-specific variability within these trends: variability in pleiotropic effects tends to increase over time, with the extent of variability depending on the evolution environment. These results suggest shifting and overlapping contributions of chance and contingency to the pleiotropic effects of adaptation, which could influence evolutionary trajectories in complex environments that fluctuate across space and time.
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Affiliation(s)
- Christopher W Bakerlee
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angela M Phillips
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard University, CambridgeCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard University, CambridgeCambridgeUnited States
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6
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Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nat Commun 2021; 12:5193. [PMID: 34465770 PMCID: PMC8408183 DOI: 10.1038/s41467-021-25440-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2021] [Indexed: 01/17/2023] Open
Abstract
Historical contingency and diminishing returns epistasis have been typically studied for relatively divergent genotypes and/or over long evolutionary timescales. Here, we use Saccharomyces cerevisiae to study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive mutational step. We further evolve three clones that arose under identical conditions from a common ancestor. We follow their evolutionary dynamics by lineage tracking and determine adaptive outcomes using fitness assays and whole genome sequencing. We find that diminishing returns manifests as smaller fitness gains during the 2nd step of adaptation compared to the 1st step, mainly due to a compressed distribution of fitness effects. We also find that the beneficial mutational spectra for the 2nd adaptive step are contingent on the 1st step, as we see both shared and diverging adaptive strategies. Finally, we find that adaptive loss-of-function mutations, such as nonsense and frameshift mutations, are less common in the second step of adaptation than in the first step. Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.
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7
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Cote-Hammarlof PA, Fragata I, Flynn J, Mavor D, Zeldovich KB, Bank C, Bolon DNA. The Adaptive Potential of the Middle Domain of Yeast Hsp90. Mol Biol Evol 2021; 38:368-379. [PMID: 32871012 PMCID: PMC7826181 DOI: 10.1093/molbev/msaa211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The distribution of fitness effects (DFEs) of new mutations across different environments quantifies the potential for adaptation in a given environment and its cost in others. So far, results regarding the cost of adaptation across environments have been mixed, and most studies have sampled random mutations across different genes. Here, we quantify systematically how costs of adaptation vary along a large stretch of protein sequence by studying the distribution of fitness effects of the same ≈2,300 amino-acid changing mutations obtained from deep mutational scanning of 119 amino acids in the middle domain of the heat shock protein Hsp90 in five environments. This region is known to be important for client binding, stabilization of the Hsp90 dimer, stabilization of the N-terminal-Middle and Middle-C-terminal interdomains, and regulation of ATPase–chaperone activity. Interestingly, we find that fitness correlates well across diverse stressful environments, with the exception of one environment, diamide. Consistent with this result, we find little cost of adaptation; on average only one in seven beneficial mutations is deleterious in another environment. We identify a hotspot of beneficial mutations in a region of the protein that is located within an allosteric center. The identified protein regions that are enriched in beneficial, deleterious, and costly mutations coincide with residues that are involved in the stabilization of Hsp90 interdomains and stabilization of client-binding interfaces, or residues that are involved in ATPase–chaperone activity of Hsp90. Thus, our study yields information regarding the role and adaptive potential of a protein sequence that complements and extends known structural information.
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Affiliation(s)
| | - Inês Fragata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Julia Flynn
- University of Massachusetts Medical School, Worcester, MA
| | - David Mavor
- University of Massachusetts Medical School, Worcester, MA
| | | | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Institute of Ecology and Evolution, University of Bern, Switzerland
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8
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Kinsler G, Geiler-Samerotte K, Petrov DA. Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation. eLife 2020; 9:e61271. [PMID: 33263280 PMCID: PMC7880691 DOI: 10.7554/elife.61271] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Building a genotype-phenotype-fitness map of adaptation is a central goal in evolutionary biology. It is difficult even when adaptive mutations are known because it is hard to enumerate which phenotypes make these mutations adaptive. We address this problem by first quantifying how the fitness of hundreds of adaptive yeast mutants responds to subtle environmental shifts. We then model the number of phenotypes these mutations collectively influence by decomposing these patterns of fitness variation. We find that a small number of inferred phenotypes can predict fitness of the adaptive mutations near their original glucose-limited evolution condition. Importantly, inferred phenotypes that matter little to fitness at or near the evolution condition can matter strongly in distant environments. This suggests that adaptive mutations are locally modular - affecting a small number of phenotypes that matter to fitness in the environment where they evolved - yet globally pleiotropic - affecting additional phenotypes that may reduce or improve fitness in new environments.
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Affiliation(s)
- Grant Kinsler
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Kerry Geiler-Samerotte
- Department of Biology, Stanford UniversityStanfordUnited States
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State UniversityTempeUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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9
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Ekkers DM, Branco dos Santos F, Mallon CA, Bruggeman F, van Doorn GS. The omnistat: A flexible continuous-culture system for prolonged experimental evolution. Methods Ecol Evol 2020; 11:932-942. [PMID: 32999708 PMCID: PMC7508058 DOI: 10.1111/2041-210x.13403] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
Microbial evolution experiments provide a powerful tool to unravel the molecular basis of adaptive evolution but their outcomes can be difficult to interpret, unless the selective forces that are applied during the experiment are carefully controlled. In this respect, experimental evolution in continuous cultures provides advantages over commonly used sequential batch-culture protocols because continuous cultures allow for more accurate control over the induced selective environment. However, commercial continuous-culture systems are large and expensive, while available DIY continuous-culture systems are not versatile enough to allow for multiple sensors and rigorous stirring.We present a modular continuous-culture system that adopts the commonly used GL45 glass laboratory bottle as a bioreactor vessel. Our design offers three advantages: first, it is equipped with a large head plate, fitting two sensors and seven input/output ports, enabling the customization of the system for many running modes (chemostat, auxostat, etc.). Second, the bioreactor is small (25-250 ml), which makes it feasible to run many replicates in parallel. Third, bioreactor modules can be coupled by uni- or bi-directional flows to induce spatiotemporal variation in selection. These features result in a particularly flexible culturing platform that facilitates the investigation of a broad range of evolutionary and ecological questions.To illustrate the versatility of our culturing system, we outline two evolution experiments that impose a temporally or spatially variable regime of selection. The first experiment illustrates how controlled temporal variation in resource availability can be utilized to select for anticipatory switching. The second experiment illustrates a spatially structured morbidostat setup that is designed to probe epistatic interactions between adaptive mutations. Furthermore, we demonstrate how sensor data can be used to stabilize selection pressures or track evolutionary adaptation.Evolution experiments in which populations are exposed to controlled spatiotemporal variation, are essential to gain insight into the process of adaptation and the mechanisms that constrain evolution. Continuous-culture systems, like the one presented here, offer control over key environmental parameters and establish a well-defined regime of selection. As such, they create the opportunity to expose evolutionary constraints in the form of phenotypic trade-offs, contributing to a mechanistic understanding of adaptive evolution.
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Affiliation(s)
- David M. Ekkers
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology GroupFaculty of ScienceSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems BiologyVU UniversityAmsterdamThe Netherlands
| | - Cyrus A. Mallon
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Frank Bruggeman
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems BiologyVU UniversityAmsterdamThe Netherlands
| | - G. Sander van Doorn
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
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10
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Cooper VS, Honsa E, Rowe H, Deitrick C, Iverson AR, Whittall JJ, Neville SL, McDevitt CA, Kietzman C, Rosch JW. Experimental Evolution In Vivo To Identify Selective Pressures during Pneumococcal Colonization. mSystems 2020; 5:e00352-20. [PMID: 32398278 PMCID: PMC7219553 DOI: 10.1128/msystems.00352-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
Experimental evolution is a powerful technique to understand how populations evolve from selective pressures imparted by the surrounding environment. With the advancement of whole-population genomic sequencing, it is possible to identify and track multiple contending genotypes associated with adaptations to specific selective pressures. This approach has been used repeatedly with model species in vitro, but only rarely in vivo Herein we report results of replicate experimentally evolved populations of Streptococcus pneumoniae propagated by repeated murine nasal colonization with the aim of identifying gene products under strong selection as well as the population genetic dynamics of infection cycles. Frameshift mutations in one gene, dltB, responsible for incorporation of d-alanine into teichoic acids on the bacterial surface, evolved repeatedly and swept to high frequency. Targeted deletions of dltB produced a fitness advantage during initial nasal colonization coupled with a corresponding fitness disadvantage in the lungs during pulmonary infection. The underlying mechanism behind the fitness trade-off between these two niches was found to be enhanced adherence to respiratory cells balanced by increased sensitivity to host-derived antimicrobial peptides, a finding recapitulated in the murine model. Additional mutations that are predicted to affect trace metal transport, central metabolism, and regulation of biofilm production and competence were also selected. These data indicate that experimental evolution can be applied to murine models of pathogenesis to gain insight into organism-specific tissue tropisms.IMPORTANCE Evolution is a powerful force that can be experimentally harnessed to gain insight into how populations evolve in response to selective pressures. Herein we tested the applicability of experimental evolutionary approaches to gain insight into how the major human pathogen Streptococcus pneumoniae responds to repeated colonization events using a murine model. These studies revealed the population dynamics of repeated colonization events and demonstrated that in vivo experimental evolution resulted in highly reproducible trajectories that reflect the environmental niche encountered during nasal colonization. Mutations impacting the surface charge of the bacteria were repeatedly selected during colonization and provided a fitness benefit in this niche that was counterbalanced by a corresponding fitness defect during lung infection. These data indicate that experimental evolution can be applied to models of pathogenesis to gain insight into organism-specific tissue tropisms.
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Affiliation(s)
- Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Erin Honsa
- St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, Tennessee, USA
| | - Hannah Rowe
- St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, Tennessee, USA
| | - Christopher Deitrick
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy R Iverson
- St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, Tennessee, USA
| | - Jonathan J Whittall
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Colin Kietzman
- St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, Tennessee, USA
| | - Jason W Rosch
- St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, Tennessee, USA
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11
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Chavhan Y, Malusare S, Dey S. Larger bacterial populations evolve heavier fitness trade-offs and undergo greater ecological specialization. Heredity (Edinb) 2020; 124:726-736. [PMID: 32203249 DOI: 10.1038/s41437-020-0308-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/09/2022] Open
Abstract
Evolutionary studies over the last several decades have invoked fitness trade-offs to explain why species prefer some environments to others. However, the effects of population size on trade-offs and ecological specialization remain largely unknown. To complicate matters, trade-offs themselves have been visualized in multiple ways in the literature. Thus, it is not clear how population size can affect the various aspects of trade-offs. To address these issues, we conducted experimental evolution with Escherichia coli populations of two different sizes in two nutritionally limited environments, and studied fitness trade-offs from three different perspectives. We found that larger populations evolved greater fitness trade-offs, regardless of how trade-offs are conceptualized. Moreover, although larger populations adapted more to their selection conditions, they also became more maladapted to other environments, ultimately paying heavier costs of adaptation. To enhance the generalizability of our results, we further investigated the evolution of ecological specialization across six different environmental pairs, and found that larger populations specialized more frequently and evolved consistently steeper reaction norms of fitness. This is the first study to demonstrate a relationship between population size and fitness trade-offs, and the results are important in understanding the population genetics of ecological specialization and vulnerability to environmental changes.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Sarthak Malusare
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.,Gaia Doctoral School, Institut des Sciences de l'Evolution (ISEM), 1093-1317 Route de Mende, 34090, Montpellier, France
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.
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12
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Soto W, Travisano M, Tolleson AR, Nishiguchi MK. Symbiont evolution during the free-living phase can improve host colonization. MICROBIOLOGY-SGM 2019; 165:174-187. [PMID: 30648935 PMCID: PMC7003651 DOI: 10.1099/mic.0.000756] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For micro-organisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether evolution during the free-living stage can be positively pleiotropic to microbial fitness in a host environment. To address this topic, the squid host Euprymna tasmanica and the marine bioluminescent bacterium Vibrio fischeri were utilized. Microbial ecological diversification in static liquid microcosms was used to simulate symbiont evolution during the free-living stage. Thirteen genetically distinct V. fischeri strains from a broad diversity of ecological sources (e.g. squid light organs, fish light organs and seawater) were examined to see if the results were reproducible in many different genetic settings. Genetic backgrounds that are closely related can be predisposed to considerable differences in how they respond to similar selection pressures. For all strains examined, new mutations with striking and facilitating effects on host colonization arose quickly during microbial evolution in the free-living stage, regardless of the ecological context under consideration for a strain’s genetic background. Microbial evolution outside a host environment promoted host range expansion, improved host colonization for a micro-organism, and diminished the negative correlation between biofilm formation and motility.
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Affiliation(s)
- William Soto
- 1College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr Williamsburg, VA 23185, USA
| | - Michael Travisano
- 2Department of Ecology, Evolution, and Behavior, University of Minnesota-Twin Cities, 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA.,3BioTechnology Institute, University of Minnesota-Twin Cities, 140 Gortner Labs, 1479 Gortner Avenue, St Paul, MN 55108, USA
| | - Alexandra Rose Tolleson
- 1College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr Williamsburg, VA 23185, USA
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13
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Sane M, Miranda JJ, Agashe D. Antagonistic pleiotropy for carbon use is rare in new mutations. Evolution 2018; 72:2202-2213. [PMID: 30095155 PMCID: PMC6203952 DOI: 10.1111/evo.13569] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 12/21/2022]
Abstract
Pleiotropic effects of mutations underlie diverse biological phenomena such as ageing and specialization. In particular, antagonistic pleiotropy ("AP": when a mutation has opposite fitness effects in different environments) generates tradeoffs, which may constrain adaptation. Models of adaptation typically assume that AP is common - especially among large-effect mutations - and that pleiotropic effect sizes are positively correlated. Empirical tests of these assumptions have focused on de novo beneficial mutations arising under strong selection. However, most mutations are actually deleterious or neutral, and may contribute to standing genetic variation that can subsequently drive adaptation. We quantified the incidence, nature, and effect size of pleiotropy for carbon utilization across 80 single mutations in Escherichia coli that arose under mutation accumulation (i.e., weak selection). Although ∼46% of the mutations were pleiotropic, only 11% showed AP; among beneficial mutations, only ∼4% showed AP. In some environments, AP was more common in large-effect mutations; and AP effect sizes across environments were often negatively correlated. Thus, AP for carbon use is generally rare (especially among beneficial mutations); is not consistently enriched in large-effect mutations; and often involves weakly deleterious antagonistic effects. Our unbiased quantification of mutational effects therefore suggests that antagonistic pleiotropy may be unlikely to cause maladaptive tradeoffs.
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Affiliation(s)
- Mrudula Sane
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
| | - Joshua John Miranda
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
| | - Deepa Agashe
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
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14
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Abstract
Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving populations are influenced by all population genetic forces, including selection, mutation, drift, and recombination, and the relative contributions of these forces may be seen as mysterious. Here, I describe why the outcomes of experimental evolution should be viewed with greater certainty because the force of selection typically dominates. Importantly, any mutant rising rapidly to high frequency in large populations must have acquired adaptive traits in the selective environment. Sequencing the genomes of these mutants can identify genes or pathways that contribute to an adaptation. I review the logic and simple mathematics why this evolve-and-resequence approach is a powerful way to find the mutations or mutation combinations that best increase fitness in any new environment.
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Affiliation(s)
- Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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15
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González-González A, Hug SM, Rodríguez-Verdugo A, Patel JS, Gaut BS. Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression. Mol Biol Evol 2017; 34:2839-2855. [PMID: 28961910 PMCID: PMC5815632 DOI: 10.1093/molbev/msx216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerous E. coli evolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2 °C. Among the eight mutations, two rho mutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of ∼20%. The rpoB mutations affected the expression of ∼1,700 genes; rho mutations affected the expression of fewer genes but most (83%) were a subset of those altered by rpoB mutants. Across the eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0 °C state. The beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, but they caused parallel phenotypic effects on gene expression and genome-wide transcriptional termination.
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Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Shaun M. Hug
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
| | - Alejandra Rodríguez-Verdugo
- Department of Environmental Systems Sciences, ETH Zürich, Zürich,
Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf,
Switzerland
| | | | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
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16
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Kacar B, Ge X, Sanyal S, Gaucher EA. Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein. J Mol Evol 2017; 84:69-84. [PMID: 28233029 PMCID: PMC5371648 DOI: 10.1007/s00239-017-9781-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/30/2017] [Indexed: 01/20/2023]
Abstract
The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.
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Affiliation(s)
- Betül Kacar
- NASA Astrobiology Institute, Mountain View, CA, 94035, USA.
- Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box-596, 75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box-596, 75124, Uppsala, Sweden
| | - Eric A Gaucher
- School of Biology, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, USA
- Petit H. Parker Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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17
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Bono LM, Smith LB, Pfennig DW, Burch CL. The emergence of performance trade‐offs during local adaptation: insights from experimental evolution. Mol Ecol 2017; 26:1720-1733. [DOI: 10.1111/mec.13979] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Lisa M. Bono
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Leno B. Smith
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - David W. Pfennig
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Christina L. Burch
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
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18
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The Genomic Architecture of Interactions Between Natural Genetic Polymorphisms and Environments in Yeast Growth. Genetics 2016; 205:925-937. [PMID: 27903611 DOI: 10.1534/genetics.116.195487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/22/2016] [Indexed: 12/26/2022] Open
Abstract
Gene-environment interaction (G×E) refers to the phenomenon that the same mutation has different phenotypic effects in different environments. Although quantitative trait loci (QTLs) exhibiting G×E have been reported, little is known about the general properties of G×E, and those of its underlying QTLs. Here, we use the genotypes of 1005 segregants from a cross between two Saccharomyces cerevisiae strains, and the growth rates of these segregants in 47 environments, to identify growth rate QTLs (gQTLs) in each environment, and QTLs that have different growth effects in each pair of environments (g×eQTLs) . The average number of g×eQTLs identified between two environments is 0.58 times the number of unique gQTLs identified in these environments, revealing a high abundance of G×E. Eighty-seven percent of g×eQTLs belong to gQTLs, supporting the practice of identifying g×eQTLs from gQTLs. Most g×eQTLs identified from gQTLs have concordant effects between environments, but, as the effect size of a mutation in one environment enlarges, the probability of antagonism in the other environment increases. Antagonistic g×eQTLs are enriched in dissimilar environments. Relative to gQTLs, g×eQTLs tend to occur at intronic and synonymous sites. The gene ontology (GO) distributions of gQTLs and g×eQTLs are significantly different, as are those of antagonistic and concordant g×eQTLs. Simulations based on the yeast data showed that ignoring G×E causes substantial missing heritability. Together, our findings reveal the genomic architecture of G×E in yeast growth, and demonstrate the importance of G×E in explaining phenotypic variation and missing heritability.
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The Fitness Effects of Spontaneous Mutations Nearly Unseen by Selection in a Bacterium with Multiple Chromosomes. Genetics 2016; 204:1225-1238. [PMID: 27672096 DOI: 10.1534/genetics.116.193060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022] Open
Abstract
Mutation accumulation (MA) experiments employ the strategy of minimizing the population size of evolving lineages to greatly reduce effects of selection on newly arising mutations. Thus, most mutations fix within MA lines independently of their fitness effects. This approach, more recently combined with genome sequencing, has detailed the rates, spectra, and biases of different mutational processes. However, a quantitative understanding of the fitness effects of mutations virtually unseen by selection has remained an untapped opportunity. Here, we analyzed the fitness of 43 sequenced MA lines of the multi-chromosome bacterium Burkholderia cenocepacia that had each undergone 5554 generations of MA and accumulated an average of 6.73 spontaneous mutations. Most lineages exhibited either neutral or deleterious fitness in three different environments in comparison with their common ancestor. The only mutational class that was significantly overrepresented in lineages with reduced fitness was the loss of the plasmid, though nonsense mutations, missense mutations, and coding insertion-deletions were also overrepresented in MA lineages whose fitness had significantly declined. Although the overall distribution of fitness effects was similar between the three environments, the magnitude and even the sign of the fitness of a number of lineages changed with the environment, demonstrating that the fitness of some genotypes was environmentally dependent. These results present an unprecedented picture of the fitness effects of spontaneous mutations in a bacterium with multiple chromosomes and provide greater quantitative support for the theory that the vast majority of spontaneous mutations are neutral or deleterious.
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