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He W, Russel J, Klincke F, Nesme J, Sørensen SJ. Insights into the ecology of the infant gut plasmidome. Nat Commun 2024; 15:6924. [PMID: 39138199 PMCID: PMC11322291 DOI: 10.1038/s41467-024-51398-3] [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: 03/01/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate the gut microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow to understand the impact of plasmids on the gut microbiome. We create a plasmid phylogenetic tree, devise a method for assigning plasmid hosts, and examine potential plasmid transfer networks. Our research discovers a wide variety of previously unidentified plasmid sequences, indicating that current databases do not fully represent the gut plasmidome. Interestingly, infants display greater plasmid diversity compared to mothers and other healthy adults. We find that Bacteroidota, a major bacterial phylum, serves as the primary host for gut plasmids and plays a dominant role in gut plasmid transfer events. Additionally, plasmids broaden the genetic capabilities of bacteria, with their influence on bacterial function becoming more apparent as children's gut microbiomes develop. This study sheds light on the role of plasmids in the infant gut microbiome, making a significant contribution to our understanding of plasmid biology.
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Affiliation(s)
- Wanli He
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Franziska Klincke
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
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2
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Horton JS, Taylor TB. Mutation bias and adaptation in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001404. [PMID: 37943288 PMCID: PMC10710837 DOI: 10.1099/mic.0.001404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Genetic mutation, which provides the raw material for evolutionary adaptation, is largely a stochastic force. However, there is ample evidence showing that mutations can also exhibit strong biases, with some mutation types and certain genomic positions mutating more often than others. It is becoming increasingly clear that mutational bias can play a role in determining adaptive outcomes in bacteria in both the laboratory and the clinic. As such, understanding the causes and consequences of mutation bias can help microbiologists to anticipate and predict adaptive outcomes. In this review, we provide an overview of the mechanisms and features of the bacterial genome that cause mutational biases to occur. We then describe the environmental triggers that drive these mechanisms to be more potent and outline the adaptive scenarios where mutation bias can synergize with natural selection to define evolutionary outcomes. We conclude by describing how understanding mutagenic genomic features can help microbiologists predict areas sensitive to mutational bias, and finish by outlining future work that will help us achieve more accurate evolutionary forecasts.
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Affiliation(s)
- James S. Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
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3
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Gitschlag BL, Cano AV, Payne JL, McCandlish DM, Stoltzfus A. Mutation and Selection Induce Correlations between Selection Coefficients and Mutation Rates. Am Nat 2023; 202:534-557. [PMID: 37792926 DOI: 10.1086/726014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractThe joint distribution of selection coefficients and mutation rates is a key determinant of the genetic architecture of molecular adaptation. Three different distributions are of immediate interest: (1) the "nominal" distribution of possible changes, prior to mutation or selection; (2) the "de novo" distribution of realized mutations; and (3) the "fixed" distribution of selectively established mutations. Here, we formally characterize the relationships between these joint distributions under the strong-selection/weak-mutation (SSWM) regime. The de novo distribution is enriched relative to the nominal distribution for the highest rate mutations, and the fixed distribution is further enriched for the most highly beneficial mutations. Whereas mutation rates and selection coefficients are often assumed to be uncorrelated, we show that even with no correlation in the nominal distribution, the resulting de novo and fixed distributions can have correlations with any combination of signs. Nonetheless, we suggest that natural systems with a finite number of beneficial mutations will frequently have the kind of nominal distribution that induces negative correlations in the fixed distribution. We apply our mathematical framework, along with population simulations, to explore joint distributions of selection coefficients and mutation rates from deep mutational scanning and cancer informatics. Finally, we consider the evolutionary implications of these joint distributions together with two additional joint distributions relevant to parallelism and the rate of adaptation.
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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5
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Horton JS, Ali SUP, Taylor TB. Transient mutation bias increases the predictability of evolution on an empirical genotype-phenotype landscape. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220043. [PMID: 37004722 PMCID: PMC10067260 DOI: 10.1098/rstb.2022.0043] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/25/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting how a population will likely navigate a genotype-phenotype landscape requires consideration of selection in combination with mutation bias, which can skew the likelihood of following a particular trajectory. Strong and persistent directional selection can drive populations to ascend toward a peak. However, with a greater number of peaks and more routes to reach them, adaptation inevitably becomes less predictable. Transient mutation bias, which operates only on one mutational step, can influence landscape navigability by biasing the mutational trajectory early in the adaptive walk. This sets an evolving population upon a particular path, constraining the number of accessible routes and making certain peaks and routes more likely to be realized than others. In this work, we employ a model system to investigate whether such transient mutation bias can reliably and predictably place populations on a mutational trajectory to the strongest selective phenotype or usher populations to realize inferior phenotypic outcomes. For this we use motile mutants evolved from ancestrally non-motile variants of the microbe Pseudomonas fluorescens SBW25, of which one trajectory exhibits significant mutation bias. Using this system, we elucidate an empirical genotype-phenotype landscape, where the hill-climbing process represents increasing strength of the motility phenotype, to reveal that transient mutation bias can facilitate rapid and predictable ascension to the strongest observed phenotype in place of equivalent and inferior trajectories. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- James S. Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Shani U. P. Ali
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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6
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [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: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L. Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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7
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Farr AD, Pesce D, Das SG, Zwart MP, de Visser JAGM. The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations. mBio 2023:e0009823. [PMID: 37129484 DOI: 10.1128/mbio.00098-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes. IMPORTANCE The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable. To this end, competition experiments were performed with a combinatorially complete set of mutants of a β-lactamase gene subject to subinhibitory concentrations of the antibiotic cefotaxime. While some mutations confer on their hosts high resistance to cefotaxime, in competition these mutations do not always confer a selective advantage. Specifically, high-resistance mutants had equivalent fitnesses despite different resistance levels and even had selective disadvantages under conditions involving spatial structure. Together, our findings suggest that the relationship between resistance level and fitness at subinhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.
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Affiliation(s)
- Andrew D Farr
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diego Pesce
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Suman G Das
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Mark P Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - J Arjan G M de Visser
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
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8
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Abstract
How do mutational biases influence the process of adaptation? A common assumption is that selection alone determines the course of adaptation from abundant preexisting variation. Yet, theoretical work shows broad conditions under which the mutation rate to a given type of variant strongly influences its probability of contributing to adaptation. Here we introduce a statistical approach to analyzing how mutation shapes protein sequence adaptation. Using large datasets from three different species, we show that the mutation spectrum has a proportional influence on the types of changes fixed in adaptation. We also show via computer simulations that a variety of factors can influence how closely the spectrum of adaptive substitutions reflects the spectrum of variants introduced by mutation. Evolutionary adaptation often occurs by the fixation of beneficial mutations. This mode of adaptation can be characterized quantitatively by a spectrum of adaptive substitutions, i.e., a distribution for types of changes fixed in adaptation. Recent work establishes that the changes involved in adaptation reflect common types of mutations, raising the question of how strongly the mutation spectrum shapes the spectrum of adaptive substitutions. We address this question with a codon-based model for the spectrum of adaptive amino acid substitutions, applied to three large datasets covering thousands of amino acid changes identified in natural and experimental adaptation in Saccharomyces cerevisiae, Escherichia coli, and Mycobacterium tuberculosis. Using species-specific mutation spectra based on prior knowledge, we find that the mutation spectrum has a proportional influence on the spectrum of adaptive substitutions in all three species. Indeed, we find that by inferring the mutation rates that best explain the spectrum of adaptive substitutions, we can accurately recover the species-specific mutation spectra. However, we also find that the predictive power of the model differs substantially between the three species. To better understand these differences, we use population simulations to explore the factors that influence how closely the spectrum of adaptive substitutions mirrors the mutation spectrum. The results show that the influence of the mutation spectrum decreases with increasing mutational supply (Nμ) and that predictive power is strongly affected by the number and diversity of beneficial mutations.
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9
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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10
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Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 2021; 371:371/6531/eaba0862. [PMID: 33602825 DOI: 10.1126/science.aba0862] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 09/16/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022]
Abstract
Although metabolism plays an active role in antibiotic lethality, antibiotic resistance is generally associated with drug target modification, enzymatic inactivation, and/or transport rather than metabolic processes. Evolution experiments of Escherichia coli rely on growth-dependent selection, which may provide a limited view of the antibiotic resistance landscape. We sequenced and analyzed E. coli adapted to representative antibiotics at increasingly heightened metabolic states. This revealed various underappreciated noncanonical genes, such as those related to central carbon and energy metabolism, which are implicated in antibiotic resistance. These metabolic alterations lead to lower basal respiration, which prevents antibiotic-mediated induction of tricarboxylic acid cycle activity, thus avoiding metabolic toxicity and minimizing drug lethality. Several of the identified metabolism-specific mutations are overrepresented in the genomes of >3500 clinical E. coli pathogens, indicating clinical relevance.
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Affiliation(s)
- Allison J Lopatkin
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA.,Department of Biology, Barnard College, New York, NY, USA.,Data Science Institute, Columbia University, New York, NY, USA.,Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Sarah C Bening
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan M Stokes
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA
| | - Michael A Kohanski
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahmed H Badran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicole J Cheney
- Ruy V. Lourenço Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jason H Yang
- Ruy V. Lourenço Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - James J Collins
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA.,Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
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11
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Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat Rev Microbiol 2021; 19:347-359. [PMID: 33469168 DOI: 10.1038/s41579-020-00497-1] [Citation(s) in RCA: 180] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 12/27/2022]
Abstract
Plasmids have a key role in bacterial ecology and evolution because they mobilize accessory genes by horizontal gene transfer. However, recent studies have revealed that the evolutionary impact of plasmids goes above and beyond their being mere gene delivery platforms. Plasmids are usually kept at multiple copies per cell, producing islands of polyploidy in the bacterial genome. As a consequence, the evolution of plasmid-encoded genes is governed by a set of rules different from those affecting chromosomal genes, and these rules are shaped by unusual concepts in bacterial genetics, such as genetic dominance, heteroplasmy or segregational drift. In this Review, we discuss recent advances that underscore the importance of plasmids in bacterial ecology and evolution beyond horizontal gene transfer. We focus on new evidence that suggests that plasmids might accelerate bacterial evolution, mainly by promoting the evolution of plasmid-encoded genes, but also by enhancing the adaptation of their host chromosome. Finally, we integrate the most relevant theoretical and empirical studies providing a global understanding of the forces that govern plasmid-mediated evolution in bacteria.
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12
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Gomez K, Bertram J, Masel J. Mutation bias can shape adaptation in large asexual populations experiencing clonal interference. Proc Biol Sci 2020; 287:20201503. [PMID: 33081612 DOI: 10.1098/rspb.2020.1503] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The extended evolutionary synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behaviour of two simultaneously adapting traits, one with larger mutation rate U, the other with larger selection coefficient s, using asexual travelling wave models. We find that adaptation is dominated by whichever trait has the faster rate of adaptation v in isolation, with the other trait subject to evolutionary stalling. Reviewing empirical claims for mutation-biased adaptation, we find that not all occur in the 'origin-fixation' regime of population genetics where v is only twice as sensitive to s as to U. In some cases, differences in U are at least ten to twelve times larger than differences in s, as needed to cause mutation-biased adaptation even in the 'multiple mutations' regime. Surprisingly, when U > s in the 'diffusive-mutation' regime, the required sensitivity ratio is also only two, despite pervasive clonal interference. Given two traits with identical v, the benefit of having higher s is surprisingly small, occurring largely when one trait is at the boundary between the origin-fixation and multiple mutations regimes.
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Affiliation(s)
- Kevin Gomez
- Graduate Interdisciplinary Program in Applied Mathematics, University of Arizona, Tucson, AZ, USA
| | - Jason Bertram
- Environmental Resilience Institute, Indiana University, Bloomington, IN, USA.,Department of Biology, Indiana University, Bloomington, IN, USA
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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13
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Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress. PLoS Genet 2020; 16:e1008649. [PMID: 32163413 PMCID: PMC7093028 DOI: 10.1371/journal.pgen.1008649] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/24/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H2O2 concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H2O2 results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H2O2 at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H2O2 induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H2O2 alters the evolution of resistance against oxygen stress. Experimental evolution of H2O2 resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients. Throughout evolution, bacteria were exposed to reactive oxygen species and evolved the ability to scavenge toxic oxygen radicals. Furthermore, multicellular organisms evolved the ability to produce such oxygen species directed against pathogens. Recent studies also suggest that ROS such as H2O2 play an important role during host gut colonisation by its microbiota. Traditionally, experiments with different antimicrobials have been carried out using fixed concentrations while in nature, including in intra-host environments, microbes are more likely to experience this type of stress in steps or gradients. Here we show that bacteria treated with sub-lethal concentrations of H2O2 (priming) survive far better than non-treated cells when they subsequently encounter a higher concentration. We also found that the 'priming' response has a protective role from lethal mutagenesis. This protection is provided by long-lived proteins that, upon priming, remain at a high level for several generations as determined by time-lapse LC-mass spectrometry. Bacteria that were primed evolved H2O2 resistance faster and to a higher level. Moreover, mutations that increase resistance to H2O2, as determined by whole-genome sequencing (WGS), do not occur in known scavenger encoding genes but in loci coding for other functions, at least in E. coli.
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14
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The fitness challenge of studying molecular adaptation. Biochem Soc Trans 2020; 47:1533-1542. [PMID: 31642877 DOI: 10.1042/bst20180626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022]
Abstract
Advances in bioinformatics and high-throughput genetic analysis increasingly allow us to predict the genetic basis of adaptive traits. These predictions can be tested and confirmed, but the molecular-level changes - i.e. the molecular adaptation - that link genetic differences to organism fitness remain generally unknown. In recent years, a series of studies have started to unpick the mechanisms of adaptation at the molecular level. In particular, this work has examined how changes in protein function, activity, and regulation cause improved organismal fitness. Key to addressing molecular adaptations is identifying systems and designing experiments that integrate changes in the genome, protein chemistry (molecular phenotype), and fitness. Knowledge of the molecular changes underpinning adaptations allow new insight into the constraints on, and repeatability of adaptations, and of the basis of non-additive interactions between adaptive mutations. Here we critically discuss a series of studies that examine the molecular-level adaptations that connect genetic changes and fitness.
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15
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Osmond MM, Otto SP, Martin G. Genetic Paths to Evolutionary Rescue and the Distribution of Fitness Effects Along Them. Genetics 2020; 214:493-510. [PMID: 31822480 PMCID: PMC7017017 DOI: 10.1534/genetics.119.302890] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
The past century has seen substantial theoretical and empirical progress on the genetic basis of adaptation. Over this same period, a pressing need to prevent the evolution of drug resistance has uncovered much about the potential genetic basis of persistence in declining populations. However, we have little theory to predict and generalize how persistence-by sufficiently rapid adaptation-might be realized in this explicitly demographic scenario. Here, we use Fisher's geometric model with absolute fitness to begin a line of theoretical inquiry into the genetic basis of evolutionary rescue, focusing here on asexual populations that adapt through de novo mutations. We show how the dominant genetic path to rescue switches from a single mutation to multiple as mutation rates and the severity of the environmental change increase. In multi-step rescue, intermediate genotypes that themselves go extinct provide a "springboard" to rescue genotypes. Comparing to a scenario where persistence is assured, our approach allows us to quantify how a race between evolution and extinction leads to a genetic basis of adaptation that is composed of fewer loci of larger effect. We hope this work brings awareness to the impact of demography on the genetic basis of adaptation.
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Affiliation(s)
- Matthew M Osmond
- Biodiversity Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sarah P Otto
- Biodiversity Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Guillaume Martin
- Institut des Sciences de l'Evolution de Montpellier UMR5554, Universite de Montpellier, CNRS-IRD-EPHE-UM, France
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16
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Anciaux Y, Lambert A, Ronce O, Roques L, Martin G. Population persistence under high mutation rate: From evolutionary rescue to lethal mutagenesis. Evolution 2019; 73:1517-1532. [DOI: 10.1111/evo.13771] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/24/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yoann Anciaux
- Bioinformatics Research Center (BiRC)Aarhus University C.F. Møllers Allé 8 8000 Aarhus Denmark
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050PSL Research University Paris France
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM)Sorbonne Université CNRS UMR 8001 Paris France
| | - Ophélie Ronce
- Institut des Sciences de l'Evolution de MontpellierUniversité de Montpellier, CNRS, IRD, EPHE Montpellier France
| | | | - Guillaume Martin
- Institut des Sciences de l'Evolution de MontpellierUniversité de Montpellier, CNRS, IRD, EPHE Montpellier France
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17
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Storz JF, Natarajan C, Signore AV, Witt CC, McCandlish DM, Stoltzfus A. The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180238. [PMID: 31154983 DOI: 10.1098/rstb.2018.0238] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: if the DNA nucleotide cytosine (C) is immediately 5' to guanine (G) on the same coding strand, then-depending on methylation status-point mutations at both sites occur at an elevated rate relative to mutations at non-CpG sites. Here, we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate haemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2 affinity in high-altitude birds. Using a dataset of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes of molecular adaptation. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Jay F Storz
- 1 School of Biological Sciences, University of Nebraska , Lincoln, NE 68588 , USA
| | | | - Anthony V Signore
- 1 School of Biological Sciences, University of Nebraska , Lincoln, NE 68588 , USA
| | - Christopher C Witt
- 2 Department of Biology, University of New Mexico , Albuquerque, NM 87131 , USA.,3 Museum of Southwestern Biology, University of New Mexico , Albuquerque, NM 87131 , USA
| | | | - Arlin Stoltzfus
- 5 Office of Data and Informatics, Material Measurement Laboratory, NIST, and Institute for Bioscience and Biotechnology Research , Rockville, MD 20850 , USA
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18
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Payne JL, Menardo F, Trauner A, Borrell S, Gygli SM, Loiseau C, Gagneux S, Hall AR. Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biol 2019; 17:e3000265. [PMID: 31083647 PMCID: PMC6532934 DOI: 10.1371/journal.pbio.3000265] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/23/2019] [Accepted: 04/26/2019] [Indexed: 11/21/2022] Open
Abstract
Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of the rates and spectra of spontaneous mutations. However, demonstrating the role of transition bias in adaptive evolution remains challenging. In particular, it is unclear whether such biases direct the evolution of bacterial pathogens adapting to treatment. We addressed this challenge by analyzing adaptive antibiotic-resistance mutations in the major human pathogen Mycobacterium tuberculosis (MTB). We found strong evidence for transition bias in two independently curated data sets comprising 152 and 208 antibiotic-resistance mutations. This was true at the level of mutational paths (distinct adaptive DNA sequence changes) and events (individual instances of the adaptive DNA sequence changes) and across different genes and gene promoters conferring resistance to a diversity of antibiotics. It was also true for mutations that do not code for amino acid changes (in gene promoters and the 16S ribosomal RNA gene rrs) and for mutations that are synonymous to each other and are therefore likely to have similar fitness effects, suggesting that transition bias can be caused by a bias in mutation supply. These results point to a central role for transition bias in determining which mutations drive adaptive antibiotic resistance evolution in a key pathogen. Some types of mutations occur more frequently than expected. This study shows that such bias —an excess of transitions over transversions—influences the evolution of antibiotic resistance in a key global pathogen, Mycobacterium tuberculosis.
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Affiliation(s)
- Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian M. Gygli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Chloe Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alex R. Hall
- Institute of Integrative Biology, ETH Zurich, Switzerland
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19
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Sackman AM, McGee LW, Morrison AJ, Pierce J, Anisman J, Hamilton H, Sanderbeck S, Newman C, Rokyta DR. Mutation-Driven Parallel Evolution during Viral Adaptation. Mol Biol Evol 2018; 34:3243-3253. [PMID: 29029274 DOI: 10.1093/molbev/msx257] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Convergent evolution has been demonstrated across all levels of biological organization, from parallel nucleotide substitutions to convergent evolution of complex phenotypes, but whether instances of convergence are the result of selection repeatedly finding the same optimal solution to a recurring problem or are the product of mutational biases remains unsettled. We generated 20 replicate lineages allowed to fix a single mutation from each of four bacteriophage genotypes under identical selective regimes to test for parallel changes within and across genotypes at the levels of mutational effect distributions and gene, protein, amino acid, and nucleotide changes. All four genotypes shared a distribution of beneficial mutational effects best approximated by a distribution with a finite upper bound. Parallel adaptation was high at the protein, gene, amino acid, and nucleotide levels, both within and among phage genotypes, with the most common first-step mutation in each background fixing on an average in 7 of 20 replicates and half of the substitutions in two of the four genotypes occurring at shared sites. Remarkably, the mutation of largest beneficial effect that fixed for each genotype was never the most common, as would be expected if parallelism were driven by selection. In fact, the mutation of smallest benefit for each genotype fixed in a total of 7 of 80 lineages, equally as often as the mutation of largest benefit, leading us to conclude that adaptation was largely mutation-driven, such that mutational biases led to frequent parallel fixation of mutations of suboptimal effect.
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Affiliation(s)
- Andrew M Sackman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Lindsey W McGee
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Jessica Pierce
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Jeremy Anisman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Hunter Hamilton
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Cayla Newman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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20
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Ibacache-Quiroga C, Oliveros JC, Couce A, Blázquez J. Parallel Evolution of High-Level Aminoglycoside Resistance in Escherichia coli Under Low and High Mutation Supply Rates. Front Microbiol 2018; 9:427. [PMID: 29615988 PMCID: PMC5867336 DOI: 10.3389/fmicb.2018.00427] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/22/2018] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance is a major concern in public health worldwide, thus there is much interest in characterizing the mutational pathways through which susceptible bacteria evolve resistance. Here we use experimental evolution to explore the mutational pathways toward aminoglycoside resistance, using gentamicin as a model, under low and high mutation supply rates. Our results show that both normo and hypermutable strains of Escherichia coli are able to develop resistance to drug dosages > 1,000-fold higher than the minimal inhibitory concentration for their ancestors. Interestingly, such level of resistance was often associated with changes in susceptibility to other antibiotics, most prominently with increased resistance to fosfomycin. Whole-genome sequencing revealed that all resistant derivatives presented diverse mutations in five common genetic elements: fhuA, fusA and the atpIBEFHAGDC, cyoABCDE, and potABCD operons. Despite the large number of mutations acquired, hypermutable strains did not pay, apparently, fitness cost. In contrast to recent studies, we found that the mutation supply rate mainly affected the speed (tempo) but not the pattern (mode) of evolution: both backgrounds acquired the mutations in the same order, although the hypermutator strain did it faster. This observation is compatible with the adaptive landscape for high-level gentamicin resistance being relatively smooth, with few local maxima; which might be a common feature among antibiotics for which resistance involves multiple loci.
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Affiliation(s)
- Claudia Ibacache-Quiroga
- Centro Nacional de Biotecnología, Madrid, Spain.,Centro de Micro-Bioinnovación, Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | | | - Alejandro Couce
- Unité Mixte de Recherche 1137, Infection, Antimicrobiens, Modélisation, Evolution, INSERM, Université Paris Diderot, Paris, France
| | - Jesus Blázquez
- Centro Nacional de Biotecnología, Madrid, Spain.,Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, Sevilla, Spain
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21
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Tack DS, Cole AC, Shroff R, Morrow BR, Ellington AD. Evolving Bacterial Fitness with an Expanded Genetic Code. Sci Rep 2018; 8:3288. [PMID: 29459649 PMCID: PMC5818497 DOI: 10.1038/s41598-018-21549-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/06/2018] [Indexed: 11/21/2022] Open
Abstract
Since the fixation of the genetic code, evolution has largely been confined to 20 proteinogenic amino acids. The development of orthogonal translation systems that allow for the codon-specific incorporation of noncanonical amino acids may provide a means to expand the code, but these translation systems cannot be simply superimposed on cells that have spent billions of years optimizing their genomes with the canonical code. We have therefore carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced through the inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical. While the evolved lineages had not resolved the ambiguous coding of the amber codon, the improvements in fitness allowed new amber codons to populate protein coding sequences.
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Affiliation(s)
- Drew S Tack
- National Institute for Standards and Technology, Gaithersburg, Maryland, USA. .,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA.
| | - Austin C Cole
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Barrett R Morrow
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
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22
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.Rainey PB, Remigi P, Farr AD, Lind PA. Darwin was right: where now for experimental evolution? Curr Opin Genet Dev 2017; 47:102-109. [DOI: 10.1016/j.gde.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/02/2023]
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23
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Abstract
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory. We find that the frequency of transitions in these data sets is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.
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Affiliation(s)
- Arlin Stoltzfus
- Genome-scale Measurements Group, Material Measurement Laboratory, NIST, and Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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24
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Affiliation(s)
- Graham Bell
- Biology Department, McGill University, Montreal, Quebec H3A 1B1, Canada
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25
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San Millan A, Escudero JA, Gifford DR, Mazel D, MacLean RC. Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria. Nat Ecol Evol 2016; 1:10. [PMID: 28812563 DOI: 10.1038/s41559-016-0010] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022]
Abstract
Plasmids are thought to play a key role in bacterial evolution by acting as vehicles for horizontal gene transfer, but the role of plasmids as catalysts of gene evolution remains unexplored. We challenged populations of Escherichia coli carrying the blaTEM-1 β-lactamase gene on either the chromosome or a multicopy plasmid (19 copies per cell) with increasing concentrations of ceftazidime. The plasmid accelerated resistance evolution by increasing the rate of appearance of novel TEM-1 mutations, thereby conferring resistance to ceftazidime, and then by amplifying the effect of TEM-1 mutations due to the increased gene dosage. Crucially, this dual effect was necessary and sufficient for the evolution of clinically relevant levels of resistance. Subsequent evolution occurred by mutations in a regulatory RNA that increased the plasmid copy number, resulting in marginal gains in ceftazidime resistance. These results uncover a role for multicopy plasmids as catalysts for the evolution of antibiotic resistance in bacteria.
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Affiliation(s)
- Alvaro San Millan
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.,Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), 28034 Madrid, Spain
| | - Jose Antonio Escudero
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr. Roux, 75015 Paris, France.,CNRS, UMR3525, 28 Rue du Dr. Roux, 75015 Paris, France
| | - Danna R Gifford
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr. Roux, 75015 Paris, France.,CNRS, UMR3525, 28 Rue du Dr. Roux, 75015 Paris, France
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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26
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Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS. Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri. Mol Biol Evol 2016; 34:93-109. [PMID: 27744412 PMCID: PMC5854121 DOI: 10.1093/molbev/msw224] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
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. Vibrio 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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Affiliation(s)
- Marcus M Dillon
- Microbiology Graduate Program, University of New Hampshire, Durham, NH
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, NC.,Department of Biology, Indiana University, Bloomington, IN
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
| | - Vaughn S Cooper
- Microbiology Graduate Program, University of New Hampshire, Durham, NH .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
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27
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Couce A, Rodríguez-Rojas A, Blázquez J. Correction to ‘Bypass of genetic constraints during mutator evolution to antibiotic resistance’. Proc Biol Sci 2016; 283:rspb.2016.1753. [DOI: 10.1098/rspb.2016.1753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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28
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Couce A, Alonso-Rodriguez N, Costas C, Oliver A, Blázquez J. Intrapopulation variability in mutator prevalence among urinary tract infection isolates of Escherichia coli. Clin Microbiol Infect 2016; 22:566.e1-7. [DOI: 10.1016/j.cmi.2016.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 11/29/2022]
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29
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Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria. Genetics 2016; 203:1369-80. [PMID: 27182949 DOI: 10.1534/genetics.115.185355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/04/2016] [Indexed: 01/05/2023] Open
Abstract
Any pathogen population sufficiently large is expected to harbor spontaneous drug-resistant mutants, often responsible for disease relapse after antibiotic therapy. It is seldom appreciated, however, that while larger populations harbor more mutants, the abundance distribution of these mutants is expected to be markedly uneven. This is because a larger population size allows early mutants to expand for longer, exacerbating their predominance in the final mutant subpopulation. Here, we investigate the extent to which this reduction in evenness can constrain the genetic diversity of spontaneous drug resistance in bacteria. Combining theory and experiments, we show that even small variations in growth rate between resistant mutants and the wild type result in orders-of-magnitude differences in genetic diversity. Indeed, only a slight fitness advantage for the mutant is enough to keep diversity low and independent of population size. These results have important clinical implications. Genetic diversity at antibiotic resistance loci can determine a population's capacity to cope with future challenges (i.e., second-line therapy). We thus revealed an unanticipated way in which the fitness effects of antibiotic resistance can affect the evolvability of pathogens surviving a drug-induced bottleneck. This insight will assist in the fight against multidrug-resistant microbes, as well as contribute to theories aimed at predicting cancer evolution.
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30
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Abstract
To what extent is the convergent evolution of protein function attributable to convergent or parallel changes at the amino acid level? The mutations that contribute to adaptive protein evolution may represent a biased subset of all possible beneficial mutations owing to mutation bias and/or variation in the magnitude of deleterious pleiotropy. A key finding is that the fitness effects of amino acid mutations are often conditional on genetic background. This context dependence (epistasis) can reduce the probability of convergence and parallelism because it reduces the number of possible mutations that are unconditionally acceptable in divergent genetic backgrounds. Here, I review factors that influence the probability of replicated evolution at the molecular level.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
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31
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Dillon MM, Rouillard NP, Van Dam B, Gallet R, Cooper VS. Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations. Evolution 2016; 70:586-99. [PMID: 26995338 DOI: 10.1111/evo.12868] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 12/17/2022]
Abstract
Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first-step beneficial mutants derived from naïve and adapted genotypes used in a long-term experimental evolution of Escherichia coli. Whole-genome sequencing was able to identify the majority of beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.
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Affiliation(s)
- Marcus M Dillon
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | - Nicholas P Rouillard
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | - Brian Van Dam
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | - Romain Gallet
- INRA - UMR BGPI Cirad TA A-54/K, Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France
| | - Vaughn S Cooper
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824. .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15219.
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32
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33
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Rodríguez-Rojas A, Makarova O, Müller U, Rolff J. Cationic Peptides Facilitate Iron-induced Mutagenesis in Bacteria. PLoS Genet 2015; 11:e1005546. [PMID: 26430769 PMCID: PMC4592263 DOI: 10.1371/journal.pgen.1005546] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/01/2015] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is the causative agent of chronic respiratory infections and is an important pathogen of cystic fibrosis patients. Adaptive mutations play an essential role for antimicrobial resistance and persistence. The factors that contribute to bacterial mutagenesis in this environment are not clear. Recently it has been proposed that cationic antimicrobial peptides such as LL-37 could act as mutagens in P. aeruginosa. Here we provide experimental evidence that mutagenesis is the product of a joint action of LL-37 and free iron. By estimating mutation rate, mutant frequencies and assessing mutational spectra in P. aeruginosa treated either with LL-37, iron or a combination of both we demonstrate that mutation rate and mutant frequency were increased only when free iron and LL-37 were present simultaneously. Colistin had the same effect. The addition of an iron chelator completely abolished this mutagenic effect, suggesting that LL-37 enables iron to enter the cells resulting in DNA damage by Fenton reactions. This was also supported by the observation that the mutational spectrum of the bacteria under LL-37-iron regime showed one of the characteristic Fenton reaction fingerprints: C to T transitions. Free iron concentration in nature and within hosts is kept at a very low level, but the situation in infected lungs of cystic fibrosis patients is different. Intermittent bleeding and damage to the epithelial cells in lungs may contribute to the release of free iron that in turn leads to generation of reactive oxygen species and deterioration of the respiratory tract, making it more susceptible to the infection.
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Affiliation(s)
- Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institute for Biology, Free University Berlin, Berlin, Germany
- * E-mail: (ARR); (JR)
| | - Olga Makarova
- Evolutionary Biology, Institute for Biology, Free University Berlin, Berlin, Germany
| | - Uta Müller
- Evolutionary Biology, Institute for Biology, Free University Berlin, Berlin, Germany
| | - Jens Rolff
- Evolutionary Biology, Institute for Biology, Free University Berlin, Berlin, Germany
- * E-mail: (ARR); (JR)
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