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Bullivant A, Lozano-Huntelman N, Tabibian K, Leung V, Armstrong D, Dudley H, Savage VM, Rodríguez-Verdugo A, Yeh PJ. Evolution Under Thermal Stress Affects Escherichia coli's Resistance to Antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582334. [PMID: 38464198 PMCID: PMC10925296 DOI: 10.1101/2024.02.27.582334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Exposure to both antibiotics and temperature changes can induce similar physiological responses in bacteria. Thus, changes in growth temperature may affect antibiotic resistance. Previous studies have found that evolution under antibiotic stress causes shifts in the optimal growth temperature of bacteria. However, little is known about how evolution under thermal stress affects antibiotic resistance. We examined 100+ heat-evolved strains of Escherichia coli that evolved under thermal stress. We asked whether evolution under thermal stress affects optimal growth temperature, if there are any correlations between evolving in high temperatures and antibiotic resistance, and if these strains' antibiotic efficacy changes depending on the local environment's temperature. We found that: (1) surprisingly, most of the heat-evolved strains displayed a decrease in optimal growth temperature and overall growth relative to the ancestor strain, (2) there were complex patterns of changes in antibiotic resistance when comparing the heat-evolved strains to the ancestor strain, and (3) there were few significant correlations among changes in antibiotic resistance, optimal growth temperature, and overall growth.
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Affiliation(s)
- Austin Bullivant
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | | | - Kevin Tabibian
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Vivien Leung
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Dylan Armstrong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Henry Dudley
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Van M. Savage
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | | | - Pamela J Yeh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
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2
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On YY, Figueroa W, Fan C, Ho PM, Bényei ÉB, Weimann A, Ruis C, Floto AR, Welch M. Impact of transient acquired hypermutability on the inter- and intra-species competitiveness of Pseudomonas aeruginosa. THE ISME JOURNAL 2023; 17:1931-1939. [PMID: 37666975 PMCID: PMC10579334 DOI: 10.1038/s41396-023-01503-z] [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: 05/31/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023]
Abstract
Once acquired, hypermutation is unrelenting, and in the long-term, leads to impaired fitness due to its cumulative impact on the genome. This raises the question of why hypermutators arise so frequently in microbial ecosystems. In this work, we explore this problem by examining how the transient acquisition of hypermutability affects inter- and intra-species competitiveness, and the response to environmental insults such as antibiotic challenge. We do this by engineering Pseudomonas aeruginosa to allow the expression of an important mismatch repair gene, mutS, to be experimentally controlled over a wide dynamic range. We show that high levels of mutS expression induce genomic stasis (hypomutation), whereas lower levels of induction lead to progressively higher rates of mutation. Whole-genome sequence analyses confirmed that the mutational spectrum of the inducible hypermutator is similar to the distinctive profile associated with mutS mutants obtained from the airways of people with cystic fibrosis (CF). The acquisition of hypermutability conferred a distinct temporal fitness advantage over the wild-type P. aeruginosa progenitor strain, in both the presence and the absence of an antibiotic selection pressure. However, over a similar time-scale, acquisition of hypermutability had little impact on the population dynamics of P. aeruginosa when grown in the presence of a competing species (Staphylococcus aureus). These data indicate that in the short term, acquired hypermutability primarily confers a competitive intra-species fitness advantage.
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Affiliation(s)
- Yue Yuan On
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Catherine Fan
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Currently based at Epoch Biodesign, Oxford, UK
| | - Pok-Man Ho
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | | | - Aaron Weimann
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Ruis
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andres R Floto
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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3
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Helsen J, Sherlock G, Dey G. Experimental evolution for cell biology. Trends Cell Biol 2023; 33:903-912. [PMID: 37188561 PMCID: PMC10592577 DOI: 10.1016/j.tcb.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
Evolutionary cell biology explores the origins, principles, and core functions of cellular features and regulatory networks through the lens of evolution. This emerging field relies heavily on comparative experiments and genomic analyses that focus exclusively on extant diversity and historical events, providing limited opportunities for experimental validation. In this opinion article, we explore the potential for experimental laboratory evolution to augment the evolutionary cell biology toolbox, drawing inspiration from recent studies that combine laboratory evolution with cell biological assays. Primarily focusing on approaches for single cells, we provide a generalizable template for adapting experimental evolution protocols to provide fresh insight into long-standing questions in cell biology.
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Affiliation(s)
- Jana Helsen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
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4
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Kugarajah V, Nisha KN, Jayakumar R, Sahabudeen S, Ramakrishnan P, Mohamed SB. Significance of microbial genome in environmental remediation. Microbiol Res 2023; 271:127360. [PMID: 36931127 DOI: 10.1016/j.micres.2023.127360] [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: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023]
Abstract
Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.
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Affiliation(s)
- Vaidhegi Kugarajah
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | | | - R Jayakumar
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | - S Sahabudeen
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram Dist, Kattankulathur, Tamil Nadu, India; Medical Team, Doctoral Institute for Evidence Based Policy, Tokyo, Japan
| | - P Ramakrishnan
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India.
| | - S B Mohamed
- Department of Materials Science, School of Technology, Central University of Tamil Nadu, Thiruvarur 610005, Tamil Nadu, India.
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Posadas-García YS, Espinosa-Soto C. Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. BMC Bioinformatics 2022; 23:509. [DOI: 10.1186/s12859-022-05067-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consensus is still lacking regarding evolutionary mechanisms involved in evolution through gene duplication as well as the conditions that affect them. We argue that a better understanding of evolution through gene duplication requires considering explicitly that genes do not act in isolation. It demands studying how the perturbation that gene duplication implies percolates through the web of gene interactions. Due to evolution’s contingent nature, the paths that lead to the final fate of duplicates must depend strongly on the early stages of gene duplication, before gene copies have accumulated distinctive changes.
Methods
Here we use a widely-known model of gene regulatory networks to study how gene duplication affects network behavior in early stages. Such networks comprise sets of genes that cross-regulate. They organize gene activity creating the gene expression patterns that give cells their phenotypic properties. We focus on how duplication affects two evolutionarily relevant properties of gene regulatory networks: mitigation of the effect of new mutations and access to new phenotypic variants through mutation.
Results
Among other observations, we find that those networks that are better at maintaining the original phenotype after duplication are usually also better at buffering the effect of single interaction mutations and that duplication tends to enhance further this ability. Moreover, the effect of mutations after duplication depends on both the kind of mutation and genes involved in it. We also found that those phenotypes that had easier access through mutation before duplication had higher chances of remaining accessible through new mutations after duplication.
Conclusion
Our results support that gene duplication often mitigates the impact of new mutations and that this effect is not merely due to changes in the number of genes. The work that we put forward helps to identify conditions under which gene duplication may enhance evolvability and robustness to mutations.
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6
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Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Nat Commun 2022; 13:5904. [PMID: 36202805 PMCID: PMC9537139 DOI: 10.1038/s41467-022-33634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
Recent experiments show that adaptive Darwinian evolution in one environment can lead to the emergence of multiple new traits that provide no immediate benefit in this environment. Such latent non-adaptive traits, however, can become adaptive in future environments. We do not know whether mutation or environment-driven selection is more important for the emergence of such traits. To find out, we evolve multiple wild-type and mutator E. coli populations under two mutation rates in simple (single antibiotic) environments and in complex (multi-antibiotic) environments. We then assay the viability of evolved populations in dozens of new environments and show that all populations become viable in multiple new environments different from those they had evolved in. The number of these new environments increases with environmental complexity but not with the mutation rate. Genome sequencing demonstrates the reason: Different environments affect pleiotropic mutations differently. Our experiments show that the selection pressure provided by an environment can be more important for the evolution of novel traits than the mutational supply experienced by a wild-type and a mutator strain of E. coli. Novel traits without immediate fitness benefit evolve frequently but we don’t know whether mutation or environment-driven selection drives this evolution. Here, using experimental evolution of E. coli populations, the authors demonstrate the importance of selection in the evolution of latent novel traits.
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7
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Zhang L, Fu Y, Zhang L, Xu Q, Yang Y, He J, Leptihn S, Loh B, Moran RA, van Schaik W, Toleman MA, Chen Q, Liu L, Yu Y, Hua X. Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure. Evol Appl 2022; 15:1045-1061. [PMID: 35899254 PMCID: PMC9309461 DOI: 10.1111/eva.13441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/16/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
OXA-23 is the predominant carbapenemase in carbapenem-resistant Acinetobacter baumannii. The co-evolutionary dynamics of A. baumannii and OXA-23-encoding plasmids are poorly understood. Here, we transformed A. baumannii ATCC 17978 with pAZJ221, a bla OXA-23-containing plasmid from clinical A. baumannii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub-inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of bla OXA-23 in pAZJ221, interfering allele dynamics, and chromosomal locus-level parallelism were observed. To characterize genotype-to-phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3' → 5') GMP-metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the effects of these mutations on fitness costs and plasmid kinetics, and the evolved plasmid containing two copies of bla OXA-23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of bla OXA-23 increased host fitness under carbapenem pressure but imposed a burden on the host in antibiotic-free media relative to the ancestral pAZJ221. Overall, our study provides a framework for the co-evolution of A. baumannii and a clinical bla OXA-23-containing plasmid in the presence of imipenem, involving early bla OXA-23 duplication followed by chromosomal adaptations that improved the fitness of plasmid-carrying cells.
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Affiliation(s)
- Linyue Zhang
- Department of Infectious Diseases, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
| | - Ying Fu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
- Department of Clinical Laboratory, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
| | - Linghong Zhang
- Department of Infectious Diseases, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
| | - Qingye Xu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
- Department of Clinical laboratory, School of MedicineAffiliated Hangzhou First People's HospitalZhejiang UniversityHangzhouChina
| | - Yunxing Yang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
- Department of Clinical laboratory, School of MedicineAffiliated Hangzhou First People's HospitalZhejiang UniversityHangzhouChina
| | - Jintao He
- Department of Infectious Diseases, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
| | - Sebastian Leptihn
- School of MedicineUniversity of Edinburgh InstituteZhejiang UniversityHangzhouChina
| | - Belinda Loh
- School of MedicineUniversity of Edinburgh InstituteZhejiang UniversityHangzhouChina
| | - Robert A. Moran
- College of Medical and Dental SciencesInstitute of Microbiology and InfectionUniversity of BirminghamBirminghamUK
| | - Willem van Schaik
- College of Medical and Dental SciencesInstitute of Microbiology and InfectionUniversity of BirminghamBirminghamUK
| | - Mark Alexander Toleman
- Department of Medical Microbiology, Division of Infection and ImmunityCardiff UniversityCardiffUK
| | - Qiong Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
- Department of Clinical laboratory, School of MedicineAffiliated Hangzhou First People's HospitalZhejiang UniversityHangzhouChina
| | - Lilin Liu
- Department of Infectious Diseases, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
| | - Yunsong Yu
- Department of Infectious Diseases, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
| | - Xiaoting Hua
- Department of Infectious Diseases, School of MedicineSir Run Run Shaw HospitalZhejiang UniversityHangzhouChina
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhouChina
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8
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Karve S, Wagner A. Multiple novel traits without immediate benefits originate in bacteria evolving on single antibiotics. Mol Biol Evol 2021; 39:6448767. [PMID: 34865131 PMCID: PMC8789282 DOI: 10.1093/molbev/msab341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
How new traits originate in evolution is a fundamental question of evolutionary biology. When such traits arise, they can either be immediately beneficial in their environment of origin, or they may become beneficial only in a future environment. Compared to immediately beneficial novel traits, novel traits without immediate benefits remain poorly studied. Here we use experimental evolution to study novel traits that are not immediately beneficial but that allow bacteria to survive in new environments. Specifically, we evolved multiple E. coli populations in five antibiotics with different mechanisms of action, and then determined their ability to grow in more than 200 environments that are different from the environment in which they evolved. Our populations evolved viability in multiple environments that contain not just clinically relevant antibiotics, but a broad range of antimicrobial molecules, such as surfactants, organic and inorganic salts, nucleotide analogues and pyridine derivatives. Genome sequencing of multiple evolved clones shows that pleiotropic mutations are important for the origin of these novel traits. Our experiments, which lasted fewer than 250 generations, demonstrate that evolution can readily create an enormous reservoir of latent traits in microbial populations. These traits can facilitate adaptive evolution in a changing world.
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Affiliation(s)
- Shraddha Karve
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, New Mexico, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600, South Africa
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9
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Martínez-Alcantar L, Orozco G, Díaz-Pérez AL, Villegas J, Reyes-De la Cruz H, García-Pineda E, Campos-García J. Participation of Acyl-Coenzyme A Synthetase FadD4 of Pseudomonas aeruginosa PAO1 in Acyclic Terpene/Fatty Acid Assimilation and Virulence by Lipid A Modification. Front Microbiol 2021; 12:785112. [PMID: 34867927 PMCID: PMC8637051 DOI: 10.3389/fmicb.2021.785112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
The pathogenic bacterium Pseudomonas aeruginosa possesses high metabolic versatility, with its effectiveness to cause infections likely due to its well-regulated genetic content. P. aeruginosa PAO1 has at least six fadD paralogous genes, which have been implicated in fatty acid (FA) degradation and pathogenicity. In this study, we used mutagenesis and a functional approach in P. aeruginosa PAO1 to determine the roles of the fadD4 gene in acyclic terpene (AT) and FA assimilation and on pathogenicity. The results indicate that fadD4 encodes a terpenoyl-CoA synthetase utilized for AT and FA assimilation. Additionally, mutations in fadD paralogs led to the modification of the quorum-sensing las/rhl systems, as well as the content of virulence factors pyocyanin, biofilm, rhamnolipids, lipopolysaccharides (LPS), and polyhydroxyalkanoates. In a Caenorhabditis elegans in vivo pathogenicity model, culture supernatants from the 24-h-grown fadD4 single mutant increased lethality compared to the PAO1 wild-type (WT) strain; however, the double mutants fadD1/fadD2, fadD1/fadD4, and fadD2/fadD4 and single mutant fadD2 increased worm survival. A correlation analysis indicated an interaction between worm death by the PAO1 strain, the fadD4 mutation, and the virulence factor LPS. Fatty acid methyl ester (FAME) analysis of LPS revealed that a proportion of the LPS and FA on lipid A were modified by the fadD4 mutation, suggesting that FadD4 is also involved in the synthesis/degradation and modification of the lipid A component of LPS. LPS isolated from the fadD4 mutant and double mutants fadD1/fadD4 and fadD2/fadD4 showed a differential behavior to induce an increase in body temperature in rats injected with LPS compared to the WT strain or from the fadD1 and fadD2 mutants. In agreement, LPS isolated from the fadD4 mutant and double mutants fadD1/fadD2 and fadD2/fadD4 increased the induction of IL-8 in rat sera, but IL1-β cytokine levels decreased in the double mutants fadD1/fadD2 and fadD1/fadD4. The results indicate that the fadD genes are implicated in the degree of pathogenicity of P. aeruginosa PAO1 induced by LPS-lipid A, suggesting that FadD4 contributes to the removal of acyl-linked FA from LPS, rendering modification in its immunogenic response associated to Toll-like receptor TLR4. The genetic redundancy of fadD is important for bacterial adaptability and pathogenicity over the host.
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Affiliation(s)
- Lorena Martínez-Alcantar
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Gabriela Orozco
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Alma Laura Díaz-Pérez
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Javier Villegas
- Laboratorio de Interacción Suelo, Planta, Microorganismo, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Homero Reyes-De la Cruz
- Laboratorio de Control Traduccional, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ernesto García-Pineda
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Jesús Campos-García
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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10
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The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms222212293. [PMID: 34830177 PMCID: PMC8622941 DOI: 10.3390/ijms222212293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/26/2022] Open
Abstract
The cell central metabolism has been shaped throughout evolutionary times when facing challenges from the availability of resources. In the budding yeast, Saccharomyces cerevisiae, a set of duplicated genes originating from an ancestral whole-genome and several coetaneous small-scale duplication events drive energy transfer through glucose metabolism as the main carbon source either by fermentation or respiration. These duplicates (~a third of the genome) have been dated back to approximately 100 MY, allowing for enough evolutionary time to diverge in both sequence and function. Gene duplication has been proposed as a molecular mechanism of biological innovation, maintaining balance between mutational robustness and evolvability of the system. However, some questions concerning the molecular mechanisms behind duplicated genes transcriptional plasticity and functional divergence remain unresolved. In this work we challenged S. cerevisiae to the use of lactic acid/lactate as the sole carbon source and performed a small adaptive laboratory evolution to this non-fermentative carbon source, determining phenotypic and transcriptomic changes. We observed growth adaptation to acidic stress, by reduction of growth rate and increase in biomass production, while the transcriptomic response was mainly driven by repression of the whole-genome duplicates, those implied in glycolysis and overexpression of ROS response. The contribution of several duplicated pairs to this carbon source switch and acidic stress is also discussed.
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11
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Chain FJJ, Assis R. BLAST from the Past: Impacts of Evolving Approaches on Studies of Evolution by Gene Duplication. Genome Biol Evol 2021; 13:evab149. [PMID: 34164667 PMCID: PMC8325566 DOI: 10.1093/gbe/evab149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 11/14/2022] Open
Abstract
In 1970, Susumu Ohno hypothesized that gene duplication was a major reservoir of adaptive innovation. However, it was not until over two decades later that DNA sequencing studies uncovered the ubiquity of gene duplication across all domains of life, highlighting its global importance in the evolution of phenotypic complexity and species diversification. Today, it seems that there are no limits to the study of evolution by gene duplication, as it has rapidly coevolved with numerous experimental and computational advances in genomics. In this perspective, we examine word stem usage in PubMed abstracts to infer how evolving discoveries and technologies have shaped the landscape of studying evolution by gene duplication, leading to a more refined understanding of its role in the emergence of novel phenotypes.
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Affiliation(s)
- Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Massachusetts, USA
| | - Raquel Assis
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, Florida, USA
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12
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Grekov I, Thöming JG, Kordes A, Häussler S. Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions. THE ISME JOURNAL 2021; 15:1165-1177. [PMID: 33273720 PMCID: PMC8115180 DOI: 10.1038/s41396-020-00841-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness in hypermutator strains of the environmental bacterium Pseudomonas aeruginosa in comparison to the host-niche-adapted Salmonella enterica. We demonstrate that P. aeruginosa, but not S. enterica, hypermutators evolve toward higher fitness under planktonic conditions. Adaptation to increased growth performance was accompanied by a reversible perturbing of the local genetic context of membrane and cell wall biosynthesis genes. Furthermore, we observed a fine-tuning of complex regulatory circuits involving multiple di-guanylate modulating enzymes that regulate the transition between fast growing planktonic and sessile biofilm-associated lifestyles. The redundancy and local specificity of the di-guanylate signaling pathways seem to allow a convergent shift toward increased growth performance across niche-adapted clonal P. aeruginosa lineages, which is accompanied by a pronounced heterogeneity of their motility, virulence, and biofilm phenotypes.
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Affiliation(s)
- Igor Grekov
- grid.7490.a0000 0001 2238 295XDepartment of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany ,grid.475435.4Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Janne Gesine Thöming
- grid.452370.70000 0004 0408 1805Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany ,grid.475435.4Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Adrian Kordes
- grid.452370.70000 0004 0408 1805Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany ,grid.10423.340000 0000 9529 9877Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Susanne Häussler
- grid.7490.a0000 0001 2238 295XDepartment of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany ,grid.452370.70000 0004 0408 1805Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany ,grid.475435.4Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.10423.340000 0000 9529 9877Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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13
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Wagner A. Information Theory Can Help Quantify the Potential of New Phenotypes to Originate as Exaptations. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.564071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Exaptations are adaptive traits that do not originate de novo but from other adaptive traits. They include complex macroscopic traits, such as the middle ear bones of mammals, which originated from reptile jaw bones, but also molecular traits, such as new binding sites of transcriptional regulators. What determines whether a trait originates de novo or as an exaptation is unknown. I here use simple information theoretic concepts to quantify a molecular phenotype’s potential to give rise to new phenotypes. These quantities rely on the amount of genetic information needed to encode a phenotype. I use these quantities to estimate the propensity of new transcription factor binding phenotypes to emerge de novo or exaptively, and do so for 187 mouse transcription factors. I also use them to quantify whether an organism’s viability in one of 10 different chemical environment is likely to arise exaptively. I show that informationally expensive traits are more likely to originate exaptively. Exaptive evolution is only sometimes favored for new transcription factor binding, but it is always favored for the informationally complex metabolic phenotypes I consider. As our ability to genotype evolving populations increases, so will our ability to understand how phenotypes of ever-increasing informational complexity originate in evolution.
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14
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Mas A, Lagadeuc Y, Vandenkoornhuyse P. Reflections on the Predictability of Evolution: Toward a Conceptual Framework. iScience 2020; 23:101736. [PMID: 33225244 PMCID: PMC7666346 DOI: 10.1016/j.isci.2020.101736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolution is generally considered to be unpredictable because genetic variations are known to occur randomly. However, remarkable patterns of repeated convergent evolution are observed, for instance, loss of pigments by organisms living in caves. Analogous phenotypes appear in similar environments, sometimes in response to similar constraints. Alongside randomness, a certain evolutionary determinism also exists, for instance, the selection of particular phenotypes subjected to particular environmental constraints in the “evolutionary funnel.” We pursue the idea that eco-evolutionary specialization is in some way determinist. The conceptual framework of phenotypic changes entailing specialization presented in this essay explains how evolution can be predicted. We also discuss how the predictability of evolution could be tested using the case of metabolic specialization through gene losses. We also put forward that microorganisms could be key models to test and possibly make headway evolutionary predictions and knowledge about evolution.
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Affiliation(s)
- Alix Mas
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Yvan Lagadeuc
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
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15
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Abstract
The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats compared to eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious traits that serve as the raw materials for genetic innovation.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Marian L Schmidt
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
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16
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Aguilar-Rodríguez J, Fares MA, Wagner A. Chaperonin overproduction and metabolic erosion caused by mutation accumulation in Escherichia coli. FEMS Microbiol Lett 2019; 366:5509575. [PMID: 31150542 DOI: 10.1093/femsle/fnz121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/30/2019] [Indexed: 12/25/2022] Open
Abstract
Bacterial cells adapting to a constant environment tend to accumulate mutations in portions of their genome that are not maintained by selection. This process has been observed in bacteria evolving under strong genetic drift, and especially in bacterial endosymbionts of insects. Here, we study this process in hypermutable Escherichia coli populations evolved through 250 single-cell bottlenecks on solid rich medium in a mutation accumulation experiment that emulates the evolution of bacterial endosymbionts. Using phenotype microarrays monitoring metabolic activity in 95 environments distinguished by their carbon sources, we observe how mutation accumulation has decreased the ability of cells to metabolize most carbon sources. We study if the chaperonin GroEL, which is naturally overproduced in bacterial endosymbionts, can ameliorate the process of metabolic erosion, because of its known ability to buffer destabilizing mutations in metabolic enzymes. Our results indicate that GroEL can slow down the negative phenotypic consequences of genome decay in some environments.
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Affiliation(s)
- José Aguilar-Rodríguez
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, New Mexico, USA
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17
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Kassen R. Experimental Evolution of Innovation and Novelty. Trends Ecol Evol 2019; 34:712-722. [PMID: 31027838 DOI: 10.1016/j.tree.2019.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/19/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
Abstract
How does novelty, a new, genetically based function, evolve? A compelling answer has been elusive because there are few model systems where both the genetic mechanisms generating novel functions and the ecological conditions that govern their origin and spread can be studied in detail. This review article considers what we have learned about the evolution of novelty from microbial selection experiments. This work reveals that the genetic routes to novelty can be more highly variable than standard models have led us to believe and underscores the importance of considering both genetics and ecology in this process.
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Affiliation(s)
- Rees Kassen
- Department of Biology, University of Ottawa, Marie-Curie, Ottawa, Ontario, K1N6N5, Canada; kassenlab.weebly.com.
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18
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Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol 2019; 15:e8462. [PMID: 30962359 PMCID: PMC6452873 DOI: 10.15252/msb.20188462] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Evidence suggests that novel enzyme functions evolved from low‐level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems‐level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non‐native substrates in Escherichia coli K‐12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non‐native substrates—D‐lyxose, D‐2‐deoxyribose, D‐arabinose, m‐tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high‐efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome‐scale model simulations of metabolism with enzyme promiscuity.
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Affiliation(s)
- Gabriela I Guzmán
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ryan A LaCroix
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Henrietta Papp
- Virological Research Group, Szentágothai Research Centre University of Pécs, Pécs, Hungary
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Richard A Notebaart
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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19
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Ligon RA, Diaz CD, Morano JL, Troscianko J, Stevens M, Moskeland A, Laman TG, Scholes E. Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise. PLoS Biol 2018; 16:e2006962. [PMID: 30457985 PMCID: PMC6245505 DOI: 10.1371/journal.pbio.2006962] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/17/2018] [Indexed: 12/25/2022] Open
Abstract
Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group—the birds-of-paradise—exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit—the “courtship phenotype.” Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness—functional overlap and interdependency—promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations. Animals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits—like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary timescales. Positive links among ornament classes suggests that selection is acting on correlated suites of traits—a composite courtship phenotype—and this integration may be partially responsible for the extreme variation in signal form that we see in birds-of-paradise.
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Affiliation(s)
- Russell A. Ligon
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Christopher D. Diaz
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America
| | - Janelle L. Morano
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America
| | - Jolyon Troscianko
- Centre for Ecology and Conservation, College of Life and Environmental Science, University of Exeter, Penryn, United Kingdom
| | - Martin Stevens
- Centre for Ecology and Conservation, College of Life and Environmental Science, University of Exeter, Penryn, United Kingdom
| | - Annalyse Moskeland
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America
| | - Timothy G. Laman
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Edwin Scholes
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America
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20
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Qi W, Cascarano MC, Schlapbach R, Katharios P, Vaughan L, Seth-Smith HMB. Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. Genome Biol Evol 2018; 10:1363-1374. [PMID: 29726925 PMCID: PMC6007542 DOI: 10.1093/gbe/evy092] [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] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity.
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Affiliation(s)
- Weihong Qi
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Maria Chiara Cascarano
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Lloyd Vaughan
- Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Helena M B Seth-Smith
- Functional Genomics Center Zurich, University of Zurich, Switzerland.,Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
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21
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Méheust R, Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E. Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Genome Biol 2018; 19:75. [PMID: 29880023 PMCID: PMC5992828 DOI: 10.1186/s13059-018-1454-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/16/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group. RESULTS We report the creation of 320 novel composite genes, both early in the evolution of Haloarchaea during haloarchaeal genesis and later in diverged haloarchaeal groups. One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points. CONCLUSIONS Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes.
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Affiliation(s)
- Raphaël Méheust
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7138 Evolution Paris Seine, 75005, Paris, France
| | - Andrew K Watson
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7138 Evolution Paris Seine, 75005, Paris, France
| | | | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Philippe Lopez
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7138 Evolution Paris Seine, 75005, Paris, France
| | - Eric Bapteste
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7138 Evolution Paris Seine, 75005, Paris, France.
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22
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Abstract
Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.
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23
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Hochberg ME, Marquet PA, Boyd R, Wagner A. Innovation: an emerging focus from cells to societies. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0414. [PMID: 29061887 DOI: 10.1098/rstb.2016.0414] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability.This article is part of the theme issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- Michael E Hochberg
- Institut des Sciences de l'Evolution, Université de Montpellier, 34095 Montpellier, France .,Santa Fe Institute, Santa Fe, NM 87501, USA.,Institute for Advanced Study in Toulouse, 31015 Toulouse, France
| | - Pablo A Marquet
- Santa Fe Institute, Santa Fe, NM 87501, USA.,Departamento de Ecologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Instituto de Ecología y Biodiversidad (IEB), Casilla 653, Santiago, Chile.,Instituto de Sistemas Complejos de Valparaíso (ISCV), Artillería 4780, Valparaíso, Chile
| | - Robert Boyd
- Santa Fe Institute, Santa Fe, NM 87501, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
| | - Andreas Wagner
- Santa Fe Institute, Santa Fe, NM 87501, USA.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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24
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Abstract
Plasmids mediate the horizontal transmission of genetic information between bacteria, facilitating their adaptation to multiple environmental conditions. An especially important example of the ability of plasmids to catalyze bacterial adaptation and evolution is their instrumental role in the global spread of antibiotic resistance, which constitutes a major threat to public health. Plasmids provide bacteria with new adaptive tools, but they also entail a metabolic burden that, in the absence of selection for plasmid-encoded traits, reduces the competitiveness of the plasmid-carrying clone. Although this fitness reduction can be alleviated over time through compensatory evolution, the initial cost associated with plasmid carriage is the main constraint on the vertical and horizontal replication of these genetic elements. The fitness effects of plasmids therefore have a crucial influence on their ability to associate with new bacterial hosts and consequently on the evolution of plasmid-mediated antibiotic resistance. However, the molecular mechanisms underlying plasmid fitness cost remain poorly understood. Here, we analyze the literature in the field and examine the potential fitness effects produced by plasmids throughout their life cycle in the host bacterium. We also explore the various mechanisms evolved by plasmids and bacteria to minimize the cost entailed by these mobile genetic elements. Finally, we discuss potential future research directions in the field.
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25
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Escudero JA, MacLean RC, San Millan A. Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance. J Vis Exp 2018. [PMID: 29781985 DOI: 10.3791/57386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Multicopy plasmids are extremely abundant in prokaryotes but their role in bacterial evolution remains poorly understood. We recently showed that the increase in gene copy number per cell provided by multicopy plasmids could accelerate the evolution of plasmid-encoded genes. In this work, we present an experimental system to test the ability of multicopy plasmids to promote gene evolution. Using simple molecular biology methods, we constructed a model system where an antibiotic resistance gene can be inserted into Escherichia coli MG1655, either in the chromosome or on a multicopy plasmid. We use an experimental evolution approach to propagate the different strains under increasing concentrations of antibiotics and we measure survival of bacterial populations over time. The choice of the antibiotic molecule and the resistance gene is so that the gene can only confer resistance through the acquisition of mutations. This "evolutionary rescue" approach provides a simple method to test the potential of multicopy plasmids to promote the acquisition of antibiotic resistance. In the next step of the experimental system, the molecular bases of antibiotic resistance are characterized. To identify mutations responsible for the acquisition of antibiotic resistance we use deep DNA sequencing of samples obtained from whole populations and clones. Finally, to confirm the role of the mutations in the gene under study, we reconstruct them in the parental background and test the resistance phenotype of the resulting strains.
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Affiliation(s)
- Jose Antonio Escudero
- Department of Animal Health, Universidad Complutense de Madrid.,Visavet Health Surveillance Centre, Universidad Complutense de Madrid
| | | | - Alvaro San Millan
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS) and CIBERESP;
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26
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Rodriguez-Beltran J, Hernandez-Beltran JCR, DelaFuente J, Escudero JA, Fuentes-Hernandez A, MacLean RC, Peña-Miller R, San Millan A. Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation. Nat Ecol Evol 2018; 2:873-881. [PMID: 29632354 PMCID: PMC6055991 DOI: 10.1038/s41559-018-0529-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/05/2018] [Indexed: 11/21/2022]
Abstract
Understanding the mechanisms governing innovation is a central element of evolutionary theory. Novel traits usually arise through mutations in existing genes, but trade-offs between new and ancestral protein functions are pervasive and constrain the evolution of innovation. Classical models posit that evolutionary innovation circumvents the constraints imposed by trade-offs through genetic amplifications, which provide functional redundancy. Bacterial multicopy plasmids provide a paradigmatic example of genetic amplification, yet their role in evolutionary innovation remains largely unexplored. Here, we reconstructed the evolution of a new trait encoded in a multicopy plasmid using TEM-1 β-lactamase as a model system. Through a combination of theory and experimentation, we show that multicopy plasmids promote the coexistence of ancestral and novel traits for dozens of generations, allowing bacteria to escape the evolutionary constraints imposed by trade-offs. Our results suggest that multicopy plasmids are excellent platforms for evolutionary innovation, contributing to explain their extreme abundance in bacteria.
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Affiliation(s)
| | | | - Javier DelaFuente
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain
| | - Jose A Escudero
- Departamento de Sanidad Animal and VISAVET, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | - Rafael Peña-Miller
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Alvaro San Millan
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain.
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
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27
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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28
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Sexton DJ, Schuster M. Nutrient limitation determines the fitness of cheaters in bacterial siderophore cooperation. Nat Commun 2017; 8:230. [PMID: 28794499 PMCID: PMC5550491 DOI: 10.1038/s41467-017-00222-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/09/2017] [Indexed: 11/28/2022] Open
Abstract
Cooperative behaviors provide a collective benefit, but are considered costly for the individual. Here, we report that these costs vary dramatically in different contexts and have opposing effects on the selection for non-cooperating cheaters. We investigate a prominent example of bacterial cooperation, the secretion of the peptide siderophore pyoverdine by Pseudomonas aeruginosa, under different nutrient-limiting conditions. Using metabolic modeling, we show that pyoverdine incurs a fitness cost only when its building blocks carbon or nitrogen are growth-limiting and are diverted from cellular biomass production. We confirm this result experimentally with a continuous-culture approach. We show that pyoverdine non-producers (cheaters) enjoy a large fitness advantage in co-culture with producers (cooperators) and spread to high frequency when limited by carbon, but not when limited by phosphorus. The principle of nutrient-dependent fitness costs has implications for the stability of cooperation in pathogenic and non-pathogenic environments, in biotechnological applications, and beyond the microbial realm. Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.
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Affiliation(s)
- D Joseph Sexton
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA.
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29
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Chu HY, Sprouffske K, Wagner A. The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient. J Evol Biol 2017; 30:1692-1711. [PMID: 28612351 DOI: 10.1111/jeb.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/11/2017] [Accepted: 06/05/2017] [Indexed: 12/11/2022]
Abstract
The benefits and detriments of recombination for adaptive evolution have been studied both theoretically and experimentally, with conflicting predictions and observations. Most pertinent experiments examine recombination's effects in an unchanging environment and do not study its genomewide effects. Here, we evolved six replicate populations of either highly recombining R+ or lowly recombining R- E. coli strains in a changing environment, by introducing the novel nutrients L-arabinose or indole into the environment. The experiment's ancestral strains are not viable on these nutrients, but 130 generations of adaptive evolution were sufficient to render them viable. Recombination conferred a more pronounced advantage to populations adapting to indole. To study the genomic changes associated with this advantage, we sequenced the genomes of 384 clones isolated from selected replicates at the end of the experiment. These genomes harbour complex changes that range from point mutations to large-scale DNA amplifications. Among several candidate adaptive mutations, those in the tryptophanase regulator tnaC stand out, because the tna operon in which it resides has a known role in indole metabolism. One of the highly recombining populations also shows a significant excess of large-scale segmental DNA amplifications that include the tna operon. This lineage also shows a unique and potentially adaptive combination of point mutations and DNA amplifications that may have originated independently from one another, to be joined later by recombination. Our data illustrate that the advantages of recombination for adaptive evolution strongly depend on the environment and that they can be associated with complex genomic changes.
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Affiliation(s)
- H-Y Chu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - K Sprouffske
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - A Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM, USA
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30
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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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