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Laehnemann D, Peña-Miller R, Rosenstiel P, Beardmore R, Jansen G, Schulenburg H. Genomics of rapid adaptation to antibiotics: convergent evolution and scalable sequence amplification. Genome Biol Evol 2014; 6:1287-301. [PMID: 24850796 PMCID: PMC4079197 DOI: 10.1093/gbe/evu106] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Evolutionary adaptation can be extremely fast, especially in response to high selection intensities. A prime example is the surge of antibiotic resistance in bacteria. The genomic underpinnings of such rapid changes may provide information on the genetic processes that enhance fast responses and the particular trait functions under selection. Here, we use experimentally evolved Escherichia coli for a detailed dissection of the genomics of rapid antibiotic resistance evolution. Our new analyses demonstrate that amplification of a sequence region containing several known antibiotic resistance genes represents a fast genomic response mechanism under high antibiotic stress, here exerted by drug combination. In particular, higher dosage of such antibiotic combinations coincided with higher copy number of the sequence region. The amplification appears to be evolutionarily costly, because amplification levels rapidly dropped after removal of the drugs. Our results suggest that amplification is a scalable process, as copy number rapidly changes in response to the selective pressure encountered. Moreover, repeated patterns of convergent evolution were found across the experimentally evolved bacterial populations, including those with lower antibiotic selection intensities. Intriguingly, convergent evolution was identified on different organizational levels, ranging from the above sequence amplification, high variant frequencies in specific genes, prevalence of individual nonsynonymous mutations to the unusual repeated occurrence of a particular synonymous mutation in Glycine codons. We conclude that constrained evolutionary trajectories underlie rapid adaptation to antibiotics. Of the identified genomic changes, sequence amplification seems to represent the most potent, albeit costly genomic response mechanism to high antibiotic stress.
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Affiliation(s)
- David Laehnemann
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
| | - Rafael Peña-Miller
- Biosciences, Geoffrey Pope Building, University of Exeter, United KingdomDepartment of Zoology, University of Oxford, United Kingdom
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, Germany
| | - Robert Beardmore
- Biosciences, Geoffrey Pope Building, University of Exeter, United Kingdom
| | - Gunther Jansen
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
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52
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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53
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Jansen G, Barbosa C, Schulenburg H. Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance. Drug Resist Updat 2014; 16:96-107. [PMID: 24594007 DOI: 10.1016/j.drup.2014.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibiotic treatments increasingly fail due to rapid dissemination of drug resistance. Comparative genomics of clinical isolates highlights the role of de novo adaptive mutations and horizontal gene transfer (HGT) in the acquisition of resistance. Yet it cannot fully describe the selective pressures and evolutionary trajectories that yielded today's problematic strains. Experimental evolution offers a compelling addition to such studies because the combination of replicated experiments under tightly controlled conditions with genomics of intermediate time points allows real-time reconstruction of evolutionary trajectories. Recent studies thus established causal links between antibiotic deployment therapies and the course and timing of mutations, the cost of resistance and the likelihood of compensating mutations. They particularly underscored the importance of long-term effects. Similar investigations incorporating horizontal gene transfer (HGT) are wanting, likely because of difficulties associated with its integration into experiments. In this review, we describe current advances in experimental evolution of antibiotic resistance and reflect on ways to incorporate horizontal gene transfer into the approach. We contend it provides a powerful tool for systematic and highly controlled dissection of evolutionary paths to antibiotic resistance that needs to be taken into account for the development of sustainable anti-bacterial treatment strategies.
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Affiliation(s)
- Gunther Jansen
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany.
| | - Camilo Barbosa
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany
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54
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Seetharaman S, Jain K. Adaptive walks and distribution of beneficial fitness effects. Evolution 2014; 68:965-75. [PMID: 24274696 DOI: 10.1111/evo.12327] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/28/2013] [Indexed: 12/25/2022]
Abstract
We study the adaptation dynamics of a maladapted asexual population on rugged fitness landscapes with many local fitness peaks. The distribution of beneficial fitness effects is assumed to belong to one of the three extreme value domains, viz. Weibull, Gumbel, and Fréchet. We work in the strong selection-weak mutation regime in which beneficial mutations fix sequentially, and the population performs an uphill walk on the fitness landscape until a local fitness peak is reached. A striking prediction of our analysis is that the fitness difference between successive steps follows a pattern of diminishing returns in the Weibull domain and accelerating returns in the Fréchet domain, as the initial fitness of the population is increased. These trends are found to be robust with respect to fitness correlations. We believe that this result can be exploited in experiments to determine the extreme value domain of the distribution of beneficial fitness effects. Our work here differs significantly from the previous ones that assume the selection coefficient to be small. On taking large effect mutations into account, we find that the length of the walk shows different qualitative trends from those derived using small selection coefficient approximation.
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Affiliation(s)
- Sarada Seetharaman
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore, 560064, India
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55
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Hietpas RT, Bank C, Jensen JD, Bolon DNA. Shifting fitness landscapes in response to altered environments. Evolution 2013; 67:3512-22. [PMID: 24299404 PMCID: PMC3855258 DOI: 10.1111/evo.12207] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/25/2013] [Indexed: 12/14/2022]
Abstract
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of adaptation. We thus demonstrate that an essential protein can harbor adaptive potential upon an environmental challenge, and report a remarkable fit of the data to a version of Fisher's geometric model that focuses on the fitness trade-offs between mutations in different environments.
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Affiliation(s)
- Ryan T. Hietpas
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Claudia Bank
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB)
| | - Jeffrey D. Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB)
| | - Daniel N. A. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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56
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Firnberg E, Ostermeier M. The genetic code constrains yet facilitates Darwinian evolution. Nucleic Acids Res 2013; 41:7420-8. [PMID: 23754851 PMCID: PMC3753648 DOI: 10.1093/nar/gkt536] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
An important goal of evolutionary biology is to understand the constraints that shape the dynamics and outcomes of evolution. Here, we address the extent to which the structure of the standard genetic code constrains evolution by analyzing adaptive mutations of the antibiotic resistance gene TEM-1 β-lactamase and the fitness distribution of codon substitutions in two influenza hemagglutinin inhibitor genes. We find that the architecture of the genetic code significantly constrains the adaptive exploration of sequence space. However, the constraints endow the code with two advantages: the ability to restrict access to amino acid mutations with a strong negative effect and, most remarkably, the ability to enrich for adaptive mutations. Our findings support the hypothesis that the standard genetic code was shaped by selective pressure to minimize the deleterious effects of mutation yet facilitate the evolution of proteins through imposing an adaptive mutation bias.
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Affiliation(s)
- Elad Firnberg
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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57
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Schenk MF, Szendro IG, Salverda ML, Krug J, de Visser JAG. Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene. Mol Biol Evol 2013; 30:1779-87. [PMID: 23676768 PMCID: PMC3708503 DOI: 10.1093/molbev/mst096] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding epistasis is central to biology. For instance, epistatic interactions determine the topography of the fitness landscape and affect the dynamics and determinism of adaptation. However, few empirical data are available, and comparing results is complicated by confounding variation in the system and the type of mutations used. Here, we take a systematic approach by quantifying epistasis in two sets of four beneficial mutations in the antibiotic resistance enzyme TEM-1 β-lactamase. Mutations in these sets have either large or small effects on cefotaxime resistance when present as single mutations. By quantifying the epistasis and ruggedness in both landscapes, we find two general patterns. First, resistance is maximal for combinations of two mutations in both fitness landscapes and declines when more mutations are added due to abundant sign epistasis and a pattern of diminishing returns with genotype resistance. Second, large-effect mutations interact more strongly than small-effect mutations, suggesting that the effect size of mutations may be an organizing principle in understanding patterns of epistasis. By fitting the data to simple phenotype resistance models, we show that this pattern may be explained by the nonlinear dependence of resistance on enzyme stability and an unknown phenotype when mutations have antagonistically pleiotropic effects. The comparison to a previously published set of mutations in the same gene with a joint benefit further shows that the enzyme's fitness landscape is locally rugged but does contain adaptive pathways that lead to high resistance.
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Affiliation(s)
| | - Ivan G. Szendro
- Institute for Theoretical Physics, University of Cologne, Köln, Germany
| | | | - Joachim Krug
- Institute for Theoretical Physics, University of Cologne, Köln, Germany
- Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Köln, Germany
| | - J. Arjan G.M. de Visser
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
- *Corresponding author: E-mail:
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58
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Schenk MF, de Visser JAGM. Predicting the evolution of antibiotic resistance. BMC Biol 2013; 11:14. [PMID: 23433262 PMCID: PMC3579749 DOI: 10.1186/1741-7007-11-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/15/2013] [Indexed: 11/30/2022] Open
Abstract
Mutations causing antibiotic resistance are often associated with a cost in the absence of antibiotics. Surprisingly, a new study found that bacteria adapting to increased temperature became resistant to rifampicin. By studying the consequences of the involved mutations in different conditions and genetic backgrounds, the authors illustrate how knowledge of two fundamental genetic properties, pleiotropy and epistasis, may help to predict the evolution of antibiotic resistance. See research article http://www.biomedcentral.com/1471-2148/13/50
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Affiliation(s)
- Martijn F Schenk
- Institute for Genetics, University of Cologne, Zulpicher Strasse 47, D-50674, Koln, Germany
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59
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Palmer AC, Kishony R. Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nat Rev Genet 2013; 14:243-8. [PMID: 23419278 DOI: 10.1038/nrg3351] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The evolution of antibiotic resistance can now be rapidly tracked with high-throughput technologies for bacterial genotyping and phenotyping. Combined with new approaches to evolve resistance in the laboratory and to characterize clinically evolved resistant pathogens, these methods are revealing the molecular basis and rate of evolution of antibiotic resistance under treatment regimens of single drugs or drug combinations. In this Progress article, we review these new tools for studying the evolution of antibiotic resistance and discuss how the genomic and evolutionary insights they provide could transform the diagnosis, treatment and predictability of antibiotic resistance in bacterial infections.
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Affiliation(s)
- Adam C Palmer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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60
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Predictability of evolution depends nonmonotonically on population size. Proc Natl Acad Sci U S A 2012; 110:571-6. [PMID: 23267075 DOI: 10.1073/pnas.1213613110] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
To gauge the relative importance of contingency and determinism in evolution is a fundamental problem that continues to motivate much theoretical and empirical research. In recent evolution experiments with microbes, this question has been explored by monitoring the repeatability of adaptive changes in replicate populations. Here, we present the results of an extensive computational study of evolutionary predictability based on an experimentally measured eight-locus fitness landscape for the filamentous fungus Aspergillus niger. To quantify predictability, we define entropy measures on observed mutational trajectories and endpoints. In contrast to the common expectation of increasingly deterministic evolution in large populations, we find that these entropies display an initial decrease and a subsequent increase with population size N, governed, respectively, by the scales Nμ and Nμ(2), corresponding to the supply rates of single and double mutations, where μ denotes the mutation rate. The amplitude of this pattern is determined by μ. We show that these observations are generic by comparing our findings for the experimental fitness landscape to simulations on simple model landscapes.
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