151
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Ghalayini M, Magnan M, Dion S, Zatout O, Bourguignon L, Tenaillon O, Lescat M. Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon. Mol Ecol 2019; 28:4470-4485. [PMID: 31482587 DOI: 10.1111/mec.15232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/24/2019] [Indexed: 02/02/2023]
Abstract
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin-treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother-to-offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated into two different diets: a regular one (chow diet, CD) and high-fat and high-sugar one (Western Diet, WD). Genome sequences revealed an early and rapid selection during the breastfeeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD; however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
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Affiliation(s)
- Mohamed Ghalayini
- IAME, INSERM, Université Paris 13, Bobigny, France.,Service de Réanimation Médico-Chirurgicale, Hôpital Avicenne, AP - HP, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Melanie Magnan
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Sara Dion
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | | | - Lucie Bourguignon
- IAME, INSERM, Université de Paris, Paris, France.,École de l'Inserm Liliane Bettencourt, Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Mathilde Lescat
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France.,Service de Microbiologie, Hôpital Avicenne, AP - HP, Bobigny, France
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152
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Shimizu K, Matsuoka Y. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv 2019; 37:107441. [PMID: 31472206 DOI: 10.1016/j.biotechadv.2019.107441] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/04/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Abstract
The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio university, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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153
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Winter DJ, Wu SH, Howell AA, Azevedo RBR, Zufall RA, Cartwright RA. accuMUlate: a mutation caller designed for mutation accumulation experiments. Bioinformatics 2019; 34:2659-2660. [PMID: 29566129 DOI: 10.1093/bioinformatics/bty165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/15/2018] [Indexed: 11/13/2022] Open
Abstract
Summary Mutation accumulation (MA) is the most widely used method for directly studying the effects of mutation. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of spontaneous mutations and use these results to understand how mutation contributes to biological processes. At present there is no software designed specifically for identifying mutations from MA lines. Here we describe accuMUlate, a probabilistic mutation caller that reflects the design of a typical MA experiment while being flexible enough to accommodate properties unique to any particular experiment. Availability and implementation accuMUlate is available from https://github.com/dwinter/accuMUlate. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David J Winter
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA.,Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Steven H Wu
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA.,Bioconsortia Inc, Davis, CA, USA
| | - Abigail A Howell
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
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154
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Wielgoss S, Wolfensberger R, Sun L, Fiegna F, Velicer GJ. Social genes are selection hotspots in kin groups of a soil microbe. Science 2019; 363:1342-1345. [PMID: 30898932 DOI: 10.1126/science.aar4416] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/20/2019] [Indexed: 12/15/2022]
Abstract
The composition of cooperative systems, including animal societies, organismal bodies, and microbial groups, reflects their past and shapes their future evolution. However, genomic diversity within many multiunit systems remains uncharacterized, limiting our ability to understand and compare their evolutionary character. We have analyzed genomic and social-phenotype variation among 120 natural isolates of the cooperative bacterium Myxococcus xanthus derived from six multicellular fruiting bodies. Each fruiting body was composed of multiple lineages radiating from a unique recent ancestor. Genomic evolution was concentrated in selection hotspots associated with evolutionary change in social phenotypes. Synonymous mutations indicated that kin lineages within the same fruiting body often first diverged from a common ancestor more than 100 generations ago. Thus, selection appears to promote endemic diversification of kin lineages that remain together over long histories of local interaction, thereby potentiating social coevolution.
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Affiliation(s)
- Sébastien Wielgoss
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
| | - Rebekka Wolfensberger
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Lei Sun
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Francesca Fiegna
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Gregory J Velicer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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155
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Natali F, Rancati G. The Mutator Phenotype: Adapting Microbial Evolution to Cancer Biology. Front Genet 2019; 10:713. [PMID: 31447882 PMCID: PMC6691094 DOI: 10.3389/fgene.2019.00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
The mutator phenotype hypothesis was postulated almost 40 years ago to reconcile the observation that while cancer cells display widespread mutational burden, acquisition of mutations in non-transformed cells is a rare event. Moreover, it also suggested that cancer evolution could be fostered by increased genome instability. Given the evolutionary conservation throughout the tree of life and the genetic tractability of model organisms, yeast and bacterial species pioneered studies to dissect the functions of genes required for genome maintenance (caretaker genes) or for cell growth control (gatekeeper genes). In this review, we first provide an overview of what we learned from model organisms about the roles of these genes and the genome instability that arises as a consequence of their dysregulation. We then discuss our current understanding of how mutator phenotypes shape the evolution of bacteria and yeast species. We end by bringing clinical evidence that lessons learned from single-cell organisms can be applied to tumor evolution.
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Affiliation(s)
- Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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156
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Martis B S, Forquet R, Reverchon S, Nasser W, Meyer S. DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria? Comput Struct Biotechnol J 2019; 17:1047-1055. [PMID: 31452857 PMCID: PMC6700405 DOI: 10.1016/j.csbj.2019.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/28/2022] Open
Abstract
DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and coordinating its transcriptional response. We present available evidence that DNA supercoiling is modulated by environmental stress conditions relevant to the infection process according to ancestral mechanisms, in zoopathogens as well as phytopathogens. We review the results of transcriptomics studies obtained in widely distant bacterial species, showing that such structural transitions of the chromosome are associated to a complex transcriptional response affecting a large fraction of the genome. Mechanisms and computational models of the transcriptional regulation by DNA supercoiling are then discussed, involving both basal interactions of RNA Polymerase with promoter DNA, and more specific interactions with regulatory proteins. A final part is specifically focused on the regulation of virulence genes within pathogenicity islands of several pathogenic bacterial species.
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Affiliation(s)
- Shiny Martis B
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
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157
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Lamrabet O, Plumbridge J, Martin M, Lenski RE, Schneider D, Hindré T. Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene. Mol Biol Evol 2019; 36:1121-1133. [PMID: 30825312 DOI: 10.1093/molbev/msz042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Transcription regulatory networks (TRNs) are of central importance for both short-term phenotypic adaptation in response to environmental fluctuations and long-term evolutionary adaptation, with global regulatory genes often being targets of natural selection in laboratory experiments. Here, we combined evolution experiments, whole-genome resequencing, and molecular genetics to investigate the driving forces, genetic constraints, and molecular mechanisms that dictate how bacteria can cope with a drastic perturbation of their TRNs. The crp gene, encoding a major global regulator in Escherichia coli, was deleted in four different genetic backgrounds, all derived from the Long-Term Evolution Experiment (LTEE) but with different TRN architectures. We confirmed that crp deletion had a more deleterious effect on growth rate in the LTEE-adapted genotypes; and we showed that the ptsG gene, which encodes the major glucose-PTS transporter, gained CRP (cyclic AMP receptor protein) dependence over time in the LTEE. We then further evolved the four crp-deleted genotypes in glucose minimal medium, and we found that they all quickly recovered from their growth defects by increasing glucose uptake. We showed that this recovery was specific to the selective environment and consistently relied on mutations in the cis-regulatory region of ptsG, regardless of the initial genotype. These mutations affected the interplay of transcription factors acting at the promoters, changed the intrinsic properties of the existing promoters, or produced new transcription initiation sites. Therefore, the plasticity of even a single promoter region can compensate by three different mechanisms for the loss of a key regulatory hub in the E. coli TRN.
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Affiliation(s)
- Otmane Lamrabet
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Jacqueline Plumbridge
- CNRS UMR8261, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-chimique, Paris, France
| | - Mikaël Martin
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI
| | | | - Thomas Hindré
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
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158
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El Houdaigui B, Forquet R, Hindré T, Schneider D, Nasser W, Reverchon S, Meyer S. Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling. Nucleic Acids Res 2019; 47:5648-5657. [PMID: 31216038 PMCID: PMC6582348 DOI: 10.1093/nar/gkz300] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 01/20/2023] Open
Abstract
DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes' local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.
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Affiliation(s)
- Bilal El Houdaigui
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Thomas Hindré
- Université Grenoble-Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Dominique Schneider
- Université Grenoble-Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
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159
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Bedhomme S, Amorós-Moya D, Valero LM, Bonifaci N, Pujana MÀ, Bravo IG. Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer. Genome Biol Evol 2019; 11:814-831. [PMID: 30753446 PMCID: PMC6427688 DOI: 10.1093/gbe/evz031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/24/2023] Open
Abstract
Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences, leading to impaired translation and reduced functionality. Here, we characterize the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different codon usage preference, of an antibiotic resistance gene. The experimental evolution was conducted with and without the corresponding antibiotic and the mutational patterns and proteomic profiles after 1,000 generations largely depend on the experimental growth conditions (e.g., mutations in antibiotic off-target genes), and on the synonymous gene version transferred (e.g., mutations in genes responsive to translational stress). The transfer of an exogenous gene extensively modifies the whole proteome, and these proteomic changes are different for the different version of the transferred gene. Additionally, we identified conspicuous changes in global regulators and in intermediate metabolism, confirmed the evolutionary ratchet generated by mutations in DNA repair genes and highlighted the plasticity of bacterial genomes accumulating large and occasionally transient duplications. Our results support a central role of HGT in fuelling evolution as a powerful mechanism promoting rapid, often dramatic genotypic and phenotypic changes. The profound reshaping of the pre-existing geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function.
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Affiliation(s)
- Stéphanie Bedhomme
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, France
| | - Dolors Amorós-Moya
- Experimental Molecular Evolution, Institute for Evolution and Biodiversity, Westfälische-Wilhelms Universität Münster, Germany
| | - Luz M Valero
- Secció de Proteomica, SCSIE Universitat de Valencia, Spain
| | - Nùria Bonifaci
- ProCURE, Catalan Institute of Oncology (ICO), Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Miquel-Àngel Pujana
- ProCURE, Catalan Institute of Oncology (ICO), Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Ignacio G Bravo
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (UMR CNRS, IRD, UM), Montpellier, France
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160
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Phenotypic plasticity of Escherichia coli upon exposure to physical stress induced by ZnO nanorods. Sci Rep 2019; 9:8575. [PMID: 31189961 PMCID: PMC6561948 DOI: 10.1038/s41598-019-44727-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/23/2019] [Indexed: 11/17/2022] Open
Abstract
Evolution of bacteria to selective chemical pressure (e.g. antibiotics) is well studied in contrast to the influence of physical stressors. Here we show that instantaneous physical stress in a homogeneous environment (without concentration gradient) induces fast adaptation of Escherichia coli. We exposed E. coli to a large number of collisions of around 105 per bacterium per second with sharp ZnO nanorods. The pressure exerted on the bacterial cell wall was up to 10 GPa and induced phenotype changes. The bacteria’s shape became more spherical, the density of their periplasm increased by around 15% and the average thickness of the cell wall by 30%. Such E. coli cells appeared almost as Gram-positive bacteria in the standard Gram staining. Additionally, we observed a combination of changes occurring at the genomic level (mutations identified in form of single nucleotide polymorphisms) and down-regulation of expression of 61 genes encoding proteins involved in β-oxidation of fatty acids, glycolysis, the citric acid cycle, as well as uptake of amino acids and enzyme cofactors. Thus, we show that bacteria undergo phenotypic changes upon instantaneous, acute physical stress without any obviously available time for gradual adaptation.
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161
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Held T, Klemmer D, Lässig M. Survival of the simplest in microbial evolution. Nat Commun 2019; 10:2472. [PMID: 31171781 PMCID: PMC6554311 DOI: 10.1038/s41467-019-10413-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/10/2019] [Indexed: 01/09/2023] Open
Abstract
The evolution of microbial and viral organisms often generates clonal interference, a mode of competition between genetic clades within a population. Here we show how interference impacts systems biology by constraining genetic and phenotypic complexity. Our analysis uses biophysically grounded evolutionary models for molecular phenotypes, such as fold stability and enzymatic activity of genes. We find a generic mode of phenotypic interference that couples the function of individual genes and the population’s global evolutionary dynamics. Biological implications of phenotypic interference include rapid collateral system degradation in adaptation experiments and long-term selection against genome complexity: each additional gene carries a cost proportional to the total number of genes. Recombination above a threshold rate can eliminate this cost, which establishes a universal, biophysically grounded scenario for the evolution of sex. In a broader context, our analysis suggests that the systems biology of microbes is strongly intertwined with their mode of evolution. In asexual populations selection at different genomic loci can interfere with each other. Here, using a biophysical model of molecular evolution the authors show that interference results in long-term degradation of molecular function, an effect that strongly depends on genome size.
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Affiliation(s)
- Torsten Held
- Institut für Biologische Physik, Universität zu Köln, Zülpicherstr. 77, 50937, Köln, Germany
| | - Daniel Klemmer
- Institut für Biologische Physik, Universität zu Köln, Zülpicherstr. 77, 50937, Köln, Germany
| | - Michael Lässig
- Institut für Biologische Physik, Universität zu Köln, Zülpicherstr. 77, 50937, Köln, Germany.
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162
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Modelling and simulating Lenski’s long-term evolution experiment. Theor Popul Biol 2019; 127:58-74. [DOI: 10.1016/j.tpb.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/15/2023]
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163
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Kosaka T, Nakajima Y, Ishii A, Yamashita M, Yoshida S, Murata M, Kato K, Shiromaru Y, Kato S, Kanasaki Y, Yoshikawa H, Matsutani M, Thanonkeo P, Yamada M. Capacity for survival in global warming: Adaptation of mesophiles to the temperature upper limit. PLoS One 2019; 14:e0215614. [PMID: 31063502 PMCID: PMC6504187 DOI: 10.1371/journal.pone.0215614] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/04/2019] [Indexed: 11/23/2022] Open
Abstract
The Intergovernmental Panel on Climate Change recommends keeping the increase in temperature to less than a two-degree increase by the end of the century, but the direct impact of global warming on ecosystems including microbes has not been investigated. Here we performed thermal adaptation of two species and three strains of mesophilic microbes for improvement of the survival upper limit of temperature, and the improvement was evaluated by a newly developed method. To understand the limitation and variation of thermal adaptation, experiments with mutators and by multiple cultures were performed. The results of experiments including genome sequencing and analysis of the characteristics of mutants suggest that these microbes bear a genomic potential to endure a 2–3°C rise in temperature but possess a limited variation of strategies for thermal adaptation.
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Affiliation(s)
- Tomoyuki Kosaka
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi, Japan
| | | | - Ayana Ishii
- Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Maiko Yamashita
- Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Saki Yoshida
- Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masayuki Murata
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Kunpei Kato
- Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuki Shiromaru
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
| | - Shun Kato
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Yu Kanasaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Japan
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hirofumi Yoshikawa
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Japan
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Japan
| | - Minenosuke Matsutani
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Pornthap Thanonkeo
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, Thailand
| | - Mamoru Yamada
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi, Japan
- * E-mail:
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164
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Bruckbauer ST, Trimarco JD, Martin J, Bushnell B, Senn KA, Schackwitz W, Lipzen A, Blow M, Wood EA, Culberson WS, Pennacchio C, Cox MM. Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection. J Bacteriol 2019; 201:e00784-18. [PMID: 30692176 PMCID: PMC6436341 DOI: 10.1128/jb.00784-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/24/2019] [Indexed: 02/06/2023] Open
Abstract
In previous work (D. R. Harris et al., J Bacteriol 191:5240-5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated that Escherichia coli could acquire substantial levels of resistance to ionizing radiation (IR) via directed evolution. Major phenotypic contributions involved adaptation of organic systems for DNA repair. We have now undertaken an extended effort to generate E. coli populations that are as resistant to IR as Deinococcus radiodurans After an initial 50 cycles of selection using high-energy electron beam IR, four replicate populations exhibit major increases in IR resistance but have not yet reached IR resistance equivalent to D. radiodurans Regular deep sequencing reveals complex evolutionary patterns with abundant clonal interference. Prominent IR resistance mechanisms involve novel adaptations to DNA repair systems and alterations in RNA polymerase. Adaptation is highly specialized to resist IR exposure, since isolates from the evolved populations exhibit highly variable patterns of resistance to other forms of DNA damage. Sequenced isolates from the populations possess between 184 and 280 mutations. IR resistance in one isolate, IR9-50-1, is derived largely from four novel mutations affecting DNA and RNA metabolism: RecD A90E, RecN K429Q, and RpoB S72N/RpoC K1172I. Additional mechanisms of IR resistance are evident.IMPORTANCE Some bacterial species exhibit astonishing resistance to ionizing radiation, with Deinococcus radiodurans being the archetype. As natural IR sources rarely exceed mGy levels, the capacity of Deinococcus to survive 5,000 Gy has been attributed to desiccation resistance. To understand the molecular basis of true extreme IR resistance, we are using experimental evolution to generate strains of Escherichia coli with IR resistance levels comparable to Deinococcus Experimental evolution has previously generated moderate radioresistance for multiple bacterial species. However, these efforts could not take advantage of modern genomic sequencing technologies. In this report, we examine four replicate bacterial populations after 50 selection cycles. Genomic sequencing allows us to follow the genesis of mutations in populations throughout selection. Novel mutations affecting genes encoding DNA repair proteins and RNA polymerase enhance radioresistance. However, more contributors are apparent.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph D Trimarco
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Duke Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joel Martin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian Bushnell
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Katherine A Senn
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Anna Lipzen
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matthew Blow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wesley S Culberson
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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165
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Changes in Intrinsic Antibiotic Susceptibility during a Long-Term Evolution Experiment with Escherichia coli. mBio 2019; 10:mBio.00189-19. [PMID: 30837336 PMCID: PMC6401480 DOI: 10.1128/mbio.00189-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High-level resistance often evolves when populations of bacteria are exposed to antibiotics, by either mutations or horizontally acquired genes. There is also variation in the intrinsic resistance levels of different bacterial strains and species that is not associated with any known history of exposure. In many cases, evolved resistance is costly to the bacteria, such that resistant types have lower fitness than their progenitors in the absence of antibiotics. Some longer-term studies have shown that bacteria often evolve compensatory changes that overcome these tradeoffs, but even those studies have typically lasted only a few hundred generations. In this study, we examine changes in the susceptibilities of 12 populations of Escherichia coli to 15 antibiotics after 2,000 and 50,000 generations without exposure to any antibiotic. On average, the evolved bacteria were more susceptible to most antibiotics than was their ancestor. The bacteria at 50,000 generations tended to be even more susceptible than after 2,000 generations, although most of the change occurred during the first 2,000 generations. Despite the general trend toward increased susceptibility, we saw diverse outcomes with different antibiotics. For streptomycin, which was the only drug to which the ancestral strain was highly resistant, none of the evolved lines showed any increased susceptibility. The independently evolved lineages often exhibited correlated responses to the antibiotics, with correlations usually corresponding to their modes of action. On balance, our study shows that bacteria with low levels of intrinsic resistance often evolve to become even more susceptible to antibiotics in the absence of corresponding selection.IMPORTANCE Resistance to antibiotics often evolves when bacteria encounter antibiotics. However, bacterial strains and species without any known exposure to these drugs also vary in their intrinsic susceptibility. In many cases, evolved resistance has been shown to be costly to the bacteria, such that resistant types have reduced competitiveness relative to their sensitive progenitors in the absence of antibiotics. In this study, we examined changes in the susceptibilities of 12 populations of Escherichia coli to 15 antibiotics after 2,000 and 50,000 generations without exposure to any drug. The evolved bacteria tended to become more susceptible to most antibiotics, with most of the change occurring during the first 2,000 generations, when the bacteria were undergoing rapid adaptation to their experimental conditions. On balance, our findings indicate that bacteria with low levels of intrinsic resistance can, in the absence of relevant selection, become even more susceptible to antibiotics.
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166
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Peng F, Widmann S, Wünsche A, Duan K, Donovan KA, Dobson RCJ, Lenski RE, Cooper TF. Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria. Mol Biol Evol 2019; 35:202-210. [PMID: 29069429 PMCID: PMC5850340 DOI: 10.1093/molbev/msx279] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment. Eight different evolved nonsynonymous mutations conferred similar fitness benefits of ∼10% when transferred into the ancestor, and these benefits were greater than the one conferred by a deletion mutation. In contrast, the same mutations had highly variable fitness effects, ranging from ∼0% to 25%, in evolved clones isolated from the populations at 20,000 generations. Two mutations that were moved into these evolved clones conferred similar fitness effects in a given clone, but different effects between the clones, indicating epistatic interactions between the evolved pykF alleles and the other mutations that had accumulated in each evolved clone. We also measured the fitness effects of six evolved pykF alleles in the same populations in which they had fixed, but at seven time points between 0 and 50,000 generations. Variation in fitness effects was high at intermediate time points, and declined to a low level at 50,000 generations, when the mean fitness effect was lowest. Our results demonstrate the importance of genetic context in determining the fitness effects of different beneficial mutations even within the same gene.
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Affiliation(s)
- Fen Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Scott Widmann
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Kristina Duan
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Katherine A Donovan
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI
| | - Tim F Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, TX
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167
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Chavhan Y, Karve S, Dey S. Adapting in larger numbers can increase the vulnerability of Escherichia coli populations to environmental changes. Evolution 2019; 73:836-846. [PMID: 30793291 DOI: 10.1111/evo.13700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/14/2019] [Indexed: 12/28/2022]
Abstract
Larger populations generally adapt faster to their existing environment. However, it is unknown if the population size experienced during evolution influences the ability to face sudden environmental changes. To investigate this issue, we subjected replicate Escherichia coli populations of different sizes to experimental evolution in an environment containing a cocktail of three antibiotics. In this environment, the ability to actively efflux molecules outside the cell is expected to be a major fitness-affecting trait. We found that all the populations eventually reached similar fitness in the antibiotic cocktail despite adapting at different speeds, with the larger populations adapting faster. Surprisingly, although efflux activity (EA) enhanced in the smaller populations, it decayed in the larger ones. The evolution of EA was largely shaped by pleiotropic responses to selection and not by drift. This demonstrates that quantitative differences in population size can lead to qualitative differences (decay/enhancement) in the fate of a character during adaptation to identical environments. Furthermore, the larger populations showed inferior fitness upon sudden exposure to several alternative stressful environments. These observations provide a novel link between population size and vulnerability to environmental changes. Counterintuitively, adapting in larger numbers can render bacterial populations more vulnerable to abrupt environmental changes.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India
| | - Shraddha Karve
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India.,Current Address: Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India
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168
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Adaptive laboratory evolution of a genome-reduced Escherichia coli. Nat Commun 2019; 10:935. [PMID: 30804335 PMCID: PMC6389913 DOI: 10.1038/s41467-019-08888-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain's systems biology.
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169
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Beckmann A, Schaum CE, Hense I. Phytoplankton adaptation in ecosystem models. J Theor Biol 2019; 468:60-71. [PMID: 30796940 DOI: 10.1016/j.jtbi.2019.01.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/03/2018] [Accepted: 01/21/2019] [Indexed: 10/27/2022]
Abstract
We compare two different approaches to model adaptation of phytoplankton through trait value changes. Both consider mutation and selection (MuSe) but differ with respect to the underlying conceptual framework. The first one (MuSe-IBM) explicitly considers a population of individuals that are subject to random mutation during cell division. The second is a deterministic multi-compartment model (MuSe-MCM) that considers numerous genotypes of the population and where mutations are treated as a transfer of biomass between neighboring genotypes (i.e., a diffusion of characteristics in trait space). Focusing on the adaptation of optimal temperature, we show model results for different scenarios: a sudden change in environmental temperature, a seasonal variation and high frequency fluctuations. In addition, we investigate the effect of different shapes of thermal reaction norms as well as the role of alternating growth and resting phases on the adaptation process. For all cases, the differences between MuSe-IBM and MuSe-MCM are found to be negligible. Both models produce a number of well-known and plausible features. While the IBM has the advantage of including more mechanistic (i.e., probabilistic) processes, the MCM is much less computationally demanding and therefore suitable for implementation in three-dimensional ecosystem models.
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Affiliation(s)
| | | | - Inga Hense
- IMF, CEN, Universität Hamburg, Grosse Elbstrasse 133, Germany.
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170
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Tonoyan L, Fleming GTA, Friel R, O'Flaherty V. Continuous culture of Escherichia coli, under selective pressure by a novel antimicrobial complex, does not result in development of resistance. Sci Rep 2019; 9:2401. [PMID: 30787338 PMCID: PMC6382887 DOI: 10.1038/s41598-019-38925-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/10/2019] [Indexed: 01/06/2023] Open
Abstract
We attempted to generate de novo resistance to a newly described biocidal complex, ITC (iodo-thiocyanate complex), and to levofloxacin (LVX) in Escherichia coli ATCC 25922, by means of selective chemostat culture. We measured resistance by determining the minimum inhibitory concentrations (MICs) for these agents. E. coli underwent 20-day parallel adaptive evolution routes under no antimicrobial selection, and gradually increasing ITC and LVX selection pressure. Long-term exposure of E. coli to ITC did not induce resistance to ITC, or cross-resistance to LVX. No distinct mutational pattern was evidenced from whole-genome sequence (WGS)-based comparisons of ITC-challenged and unchallenged bacterial populations. Moreover, the exposed E. coli population could not survive a 2 × MIC challenge of ITC. By contrast, resistance to LVX was rapidly induced (on day 1 the MIC had increased 16-fold), selected for (by day 14 the MIC had increased 64-fold) and enriched with a highly characteristic genome mutational pattern. WGS of this evolving population revealed that the majority of mutations appeared in the genes of LVX target proteins (GyrA, ParC, ParE) and drug influx (OmpF). This study suggests that the usage of ITC may not trigger the emergence of facile resistance or cross-resistance, in contrast to common antibiotics.
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Affiliation(s)
- Lilit Tonoyan
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland.
| | - Gerard T A Fleming
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Ruairi Friel
- Westway Health, Unit 120, Business Innovation Centre, National University of Ireland Galway, Galway, Ireland
| | - Vincent O'Flaherty
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland.
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171
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Ellison C, Bachtrog D. Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila. PLoS Biol 2019; 17:e3000094. [PMID: 30742611 PMCID: PMC6417741 DOI: 10.1371/journal.pbio.3000094] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/14/2019] [Accepted: 01/18/2019] [Indexed: 11/18/2022] Open
Abstract
The repeatability or predictability of evolution is a central question in evolutionary biology and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage-compensation male-specific lethal (MSL) complex to study the mutational paths that have led to the acquisition of hundreds of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the D. melanica and D. robusta species groups by genome sequencing and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve hundreds of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element (TE) insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes and appears to be contingent on genomic properties of that species, such as simple repeat or TE density. This establishes the "genomic environment" as an important determinant in predicting the outcome of evolutionary adaptations.
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Affiliation(s)
- Christopher Ellison
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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172
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Existing Host Range Mutations Constrain Further Emergence of RNA Viruses. J Virol 2019; 93:JVI.01385-18. [PMID: 30463962 DOI: 10.1128/jvi.01385-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
RNA viruses are capable of rapid host shifting, typically due to a point mutation that confers expanded host range. As additional point mutations are necessary for further expansions, epistasis among host range mutations can potentially affect the mutational neighborhood and frequency of niche expansion. We mapped the mutational neighborhood of host range expansion using three genotypes of the double-stranded RNA (dsRNA) bacteriophage φ6 (wild type and two isogenic host range mutants) on the novel host Pseudomonas syringae pv. atrofaciens. Both Sanger sequencing of 50 P. syringae pv. atrofaciens mutant clones for each genotype and population Illumina sequencing revealed the same high-frequency mutations allowing infection of P. syringae pv. atrofaciens. Wild-type φ6 had at least nine different ways of mutating to enter the novel host, eight of which are in p3 (host attachment protein gene), and 13/50 clones had unchanged p3 genes. However, the two isogenic mutants had dramatically restricted neighborhoods: only one or two mutations, all in p3. Deep sequencing revealed that wild-type clones without mutations in p3 likely had changes in p12 (morphogenic protein), a region that was not polymorphic for the two isogenic host range mutants. Sanger sequencing confirmed that 10/13 of the wild-type φ6 clones had nonsynonymous mutations in p12, and 2 others had point mutations in p9 and p5. None of these genes had previously been associated with host range expansion in φ6. We demonstrate, for the first time, epistatic constraint in an RNA virus due to host range mutations themselves, which has implications for models of serial host range expansion.IMPORTANCE RNA viruses mutate rapidly and frequently expand their host ranges to infect novel hosts, leading to serial host shifts. Using an RNA bacteriophage model system (Pseudomonas phage φ6), we studied the impact of preexisting host range mutations on another host range expansion. Results from both clonal Sanger and Illumina sequencing show that extant host range mutations dramatically narrow the neighborhood of potential host range mutations compared to that of wild-type φ6. This research suggests that serial host-shifting viruses may follow a small number of molecular paths to enter additional novel hosts. We also identified new genes involved in φ6 host range expansion, expanding our knowledge of this important model system in experimental evolution.
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173
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Abstract
The composite members of the microbiota face a range of selective pressures and must adapt to persist in the host. We highlight recent work characterizing the evolution and transfer of genetic information across nested scales of host-associated microbiota, which enable resilience to biotic and abiotic perturbations. At the strain level, we consider the preservation and diversification of adaptive information in progeny lineages. At the community level, we consider genetic exchange between distinct microbes in the ecosystem. Finally, we frame microbiomes as open systems subject to acquisition of novel information from foreign ecosystems through invasion by outsider microbes.
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174
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Chavhan YD, Ali SI, Dey S. Larger Numbers Can Impede Adaptation in Asexual Populations despite Entailing Greater Genetic Variation. Evol Biol 2019. [DOI: 10.1007/s11692-018-9467-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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175
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Liu R, Liang L, Choudhury A, Garst AD, Eckert CA, Oh EJ, Winkler J, Gill RT. Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production. Metab Eng 2019; 51:50-58. [DOI: 10.1016/j.ymben.2018.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/29/2018] [Accepted: 07/16/2018] [Indexed: 01/24/2023]
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176
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Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol 2019; 17:e3000102. [PMID: 30673701 PMCID: PMC6361464 DOI: 10.1371/journal.pbio.3000102] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.
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Affiliation(s)
- Nandita R. Garud
- Gladstone Institutes, San Francisco, California, United States of America
| | - Benjamin H. Good
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
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177
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Dolson EL, Vostinar AE, Wiser MJ, Ofria C. The MODES Toolbox: Measurements of Open-Ended Dynamics in Evolving Systems. ARTIFICIAL LIFE 2019; 25:50-73. [PMID: 30933626 DOI: 10.1162/artl_a_00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Building more open-ended evolutionary systems can simultaneously advance our understanding of biology, artificial life, and evolutionary computation. In order to do so, however, we need a way to determine when we are moving closer to this goal. We propose a set of metrics that allow us to measure a system's ability to produce commonly-agreed-upon hallmarks of open-ended evolution: change potential, novelty potential, complexity potential, and ecological potential. Our goal is to make these metrics easy to incorporate into a system, and comparable across systems so that we can make coherent progress as a field. To this end, we provide detailed algorithms (including C++ implementations) for these metrics that should be easy to incorporate into existing artificial life systems. Furthermore, we expect this toolbox to continue to grow as researchers implement these metrics in new languages and as the community reaches consensus about additional hallmarks of open-ended evolution. For example, we would welcome a measurement of a system's potential to produce major transitions in individuality. To confirm that our metrics accurately measure the hallmarks we are interested in, we test them on two very different experimental systems: NK landscapes and the Avida digital evolution platform. We find that our observed results are consistent with our prior knowledge about these systems, suggesting that our proposed metrics are effective and should generalize to other systems.
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Affiliation(s)
- Emily L Dolson
- Michigan State University, BEACON Center for the Study of Evolution in Action, Department of Computer Science and Engineering Program in Ecology, Evolutionary Biology, and Behavior.
| | | | - Michael J Wiser
- Michigan State University, BEACON Center for the Study of Evolution in Action Program in Ecology, Evolutionary Biology, and Behavior.
| | - Charles Ofria
- Michigan State University, BEACON Center for the Study of Evolution in Action, Department of Computer Science and Engineering Program in Ecology, Evolutionary Biology, and Behavior.
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178
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The dynamics of adaptive genetic diversity during the early stages of clonal evolution. Nat Ecol Evol 2018; 3:293-301. [PMID: 30598529 DOI: 10.1038/s41559-018-0758-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
Abstract
The dynamics of genetic diversity in large clonally evolving cell populations are poorly understood, despite having implications for the treatment of cancer and microbial infections. Here, we combine barcode lineage tracking, sequencing of adaptive clones and mathematical modelling of mutational dynamics to understand adaptive diversity changes during experimental evolution of Saccharomyces cerevisiae under nitrogen and carbon limitation. We find that, despite differences in beneficial mutational mechanisms and fitness effects, early adaptive genetic diversity increases predictably, driven by the expansion of many single-mutant lineages. However, a crash in adaptive diversity follows, caused by highly fit double-mutant 'jackpot' clones that are fed from exponentially growing single mutants, a process closely related to the classic Luria-Delbrück experiment. The diversity crash is likely to be a general feature of asexual evolution with clonal interference; however, both its timing and magnitude are stochastic and depend on the population size, the distribution of beneficial fitness effects and patterns of epistasis.
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179
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Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment. Proc Natl Acad Sci U S A 2018; 116:187-192. [PMID: 30563853 DOI: 10.1073/pnas.1718997115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations-those requiring the independent acquisition of multiple new genes-can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of the E. coli clade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combined E. coli pangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of the E. coli lineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.
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180
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Leiser OP, Blackburn JK, Hadfield TL, Kreuzer HW, Wunschel DS, Bruckner-Lea CJ. Laboratory strains of Bacillus anthracis exhibit pervasive alteration in expression of proteins related to sporulation under laboratory conditions relative to genetically related wild strains. PLoS One 2018; 13:e0209120. [PMID: 30557394 PMCID: PMC6296524 DOI: 10.1371/journal.pone.0209120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
Abstract
The spore forming pathogen Bacillus anthracis is the etiologic agent of anthrax in humans and animals. It cycles through infected hosts as vegetative cells and is eventually introduced into the environment where it generates an endospore resistant to many harsh conditions. The endospores are subsequently taken up by another host to begin the next cycle. Outbreaks of anthrax occur regularly worldwide in wildlife and livestock, and the potential for human infection exists whenever humans encounter infected animals. It is also possible to encounter intentional releases of anthrax spores, as was the case in October 2001. Consequently, it is important to be able to rapidly establish the provenance of infectious strains of B. anthracis. Here, we compare protein expression in seven low-passage wild isolates and four laboratory strains of B. anthracis grown under identical conditions using LC-MS/MS proteomic analysis. Of the 1,023 total identified proteins, 96 had significant abundance differences between wild and laboratory strains. Of those, 28 proteins directly related to sporulation were upregulated in wild isolates, with expression driven by Spo0A, CodY, and AbrB/ScoC. In addition, we observed evidence of changes in cell division and fatty acid biosynthesis between the two classes of strains, despite being grown under identical experimental conditions. These results suggest wild B. anthracis cells are more highly tuned to sporulate than their laboratory cousins, and this difference should be exploited as a method to differentiate between laboratory and low passage wild strains isolated during an anthrax outbreak. This knowledge should distinguish between intentional releases and exposure to strains in nature, providing a basis for the type of response by public health officials and investigators.
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Affiliation(s)
- Owen P. Leiser
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason K. Blackburn
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Ted L. Hadfield
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David S. Wunschel
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Cindy J. Bruckner-Lea
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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181
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Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC. Quantification of somatic mutation flow across individual cell division events by lineage sequencing. Genome Res 2018; 28:1901-1918. [PMID: 30459213 PMCID: PMC6280753 DOI: 10.1101/gr.238543.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/27/2018] [Indexed: 02/06/2023]
Abstract
Mutation data reveal the dynamic equilibrium between DNA damage and repair processes in cells and are indispensable to the understanding of age-related diseases, tumor evolution, and the acquisition of drug resistance. However, available genome-wide methods have a limited ability to resolve rare somatic variants and the relationships between these variants. Here, we present lineage sequencing, a new genome sequencing approach that enables somatic event reconstruction by providing quality somatic mutation call sets with resolution as high as the single-cell level in subject lineages. Lineage sequencing entails sampling single cells from a population and sequencing subclonal sample sets derived from these cells such that knowledge of relationships among the cells can be used to jointly call variants across the sample set. This approach integrates data from multiple sequence libraries to support each variant and precisely assigns mutations to lineage segments. We applied lineage sequencing to a human colon cancer cell line with a DNA polymerase epsilon (POLE) proofreading deficiency (HT115) and a human retinal epithelial cell line immortalized by constitutive telomerase expression (RPE1). Cells were cultured under continuous observation to link observed single-cell phenotypes with single-cell mutation data. The high sensitivity, specificity, and resolution of the data provide a unique opportunity for quantitative analysis of variation in mutation rate, spectrum, and correlations among variants. Our data show that mutations arrive with nonuniform probability across sublineages and that DNA lesion dynamics may cause strong correlations between certain mutations.
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Affiliation(s)
- Yehuda Brody
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Robert J Kimmerling
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, USA
| | - Yosef E Maruvka
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MGH Cancer Center and Department of Pathology, Boston, Massachusetts 02114, USA
| | - David Benjamin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joshua J Elacqua
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
| | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MGH Cancer Center and Department of Pathology, Boston, Massachusetts 02114, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kent W Mouw
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kristjana Frangaj
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Gad Getz
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MGH Cancer Center and Department of Pathology, Boston, Massachusetts 02114, USA
| | - Scott R Manalis
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
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182
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McGenity TJ. 2038 – When microbes rule the Earth. Environ Microbiol 2018; 20:4213-4220. [DOI: 10.1111/1462-2920.14449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Terry J. McGenity
- School of Biological SciencesUniversity of Essex Colchester United Kingdom
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183
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Dragoš A, Lakshmanan N, Martin M, Horváth B, Maróti G, Falcón García C, Lieleg O, Kovács ÁT. Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms. FEMS Microbiol Ecol 2018; 93:4604779. [PMID: 29126191 DOI: 10.1093/femsec/fix155] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discovered that-similarly to other species-B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Nivedha Lakshmanan
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Balázs Horváth
- Seqomics Biotechnology Ltd, Vállalkozók útja 7, Mórahalom 6782, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
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184
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Flynn JM, Lower SE, Barbash DA, Clark AG. Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii. Genome Biol Evol 2018; 10:1673-1686. [PMID: 29931069 PMCID: PMC6041958 DOI: 10.1093/gbe/evy123] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/15/2022] Open
Abstract
The mutational patterns of large tandem arrays of short sequence repeats remain largely unknown, despite observations of their high levels of variation in sequence and genomic abundance within and between species. Many factors can influence the dynamics of tandem repeat evolution; however, their evolution has only been examined over a limited phylogenetic sample of taxa. Here, we use publicly available whole-genome sequencing data of 85 haploid mutation accumulation lines derived from six geographically diverse Chlamydomonas reinhardtii isolates to investigate genome-wide mutation rates and patterns in tandem repeats in this species. We find that tandem repeat composition differs among ancestral strains, both in genome-wide abundance and presence/absence of individual repeats. Estimated mutation rates (repeat copy number expansion and contraction) were high, averaging 4.3×10−4 per generation per single unit copy. Although orders of magnitude higher than other types of mutation previously reported in C. reinhardtii, these tandem repeat mutation rates were one order of magnitude lower than what has recently been found in Daphnia pulex, even after correcting for lower overall genome-wide satellite abundance in C. reinhardtii. Most high-abundance repeats were related to others by a single mutational step. Correlations of repeat copy number changes within genomes revealed clusters of closely related repeats that were strongly correlated positively or negatively, and similar patterns of correlation arose independently in two different mutation accumulation experiments. Together, these results paint a dynamic picture of tandem repeat evolution in this unicellular alga.
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Sarah E Lower
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
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185
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Bolnick DI, Barrett RD, Oke KB, Rennison DJ, Stuart YE. (Non)Parallel Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062240] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parallel evolution across replicate populations has provided evolutionary biologists with iconic examples of adaptation. When multiple populations colonize seemingly similar habitats, they may evolve similar genes, traits, or functions. Yet, replicated evolution in nature or in the laboratory often yields inconsistent outcomes: Some replicate populations evolve along highly similar trajectories, whereas other replicate populations evolve to different extents or in distinct directions. To understand these heterogeneous outcomes, biologists are increasingly treating parallel evolution not as a binary phenomenon but rather as a quantitative continuum ranging from parallel to nonparallel. By measuring replicate populations’ positions along this (non)parallel continuum, we can test hypotheses about evolutionary and ecological factors that influence the extent of repeatable evolution. We review evidence regarding the manifestation of (non)parallel evolution in the laboratory, in natural populations, and in applied contexts such as cancer. We enumerate the many genetic, ecological, and evolutionary processes that contribute to variation in the extent of parallel evolution.
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Affiliation(s)
- Daniel I. Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Current affiliation: Department of Ecology and Evolution, University of Connecticut, Storrs, Connecticut 06268, USA
| | | | - Krista B. Oke
- Redpath Museum, McGill University, Montreal, Quebec H3A 2K6, Canada
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95060, USA
| | - Diana J. Rennison
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yoel E. Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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186
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Biot-Pelletier D, Pinel D, Larue K, Martin VJJ. Determinants of selection in yeast evolved by genome shuffling. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:282. [PMID: 30356826 PMCID: PMC6190656 DOI: 10.1186/s13068-018-1283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Genome shuffling (GS) is a widely adopted methodology for the evolutionary engineering of desirable traits in industrially relevant microorganisms. We have previously used genome shuffling to generate a strain of Saccharomyces cerevisiae that is tolerant to the growth inhibitors found in a lignocellulosic hydrolysate. In this study, we expand on previous work by performing a population-wide genomic survey of our genome shuffling experiment and dissecting the molecular determinants of the evolved phenotype. RESULTS Whole population whole-genome sequencing was used to survey mutations selected during the experiment and extract allele frequency time series. Using growth curve assays on single point mutants and backcrossed derivatives, we explored the genetic architecture of the selected phenotype and detected examples of epistasis. Our results reveal cohorts of strongly correlated mutations, suggesting prevalent genetic hitchhiking and the presence of pre-existing founder mutations. From the patterns of apparent selection and the results of direct phenotypic assays, our results identify key driver mutations and deleterious hitchhikers. CONCLUSIONS We use these data to propose a model of inhibitor tolerance in our GS mutants. Our results also suggest a role for compensatory evolution and epistasis in our genome shuffling experiment and illustrate the impact of historical contingency on the outcomes of evolutionary engineering.
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Affiliation(s)
- Damien Biot-Pelletier
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Lallemand Inc., Montréal, QC H4P 2R2 Canada
| | - Dominic Pinel
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Amyris Inc, Emeryville, CA 94608 USA
| | - Kane Larue
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Charles River Laboratories, Senneville, QC H9X 3R3 Canada
| | - Vincent J. J. Martin
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
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187
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Good BH, Hallatschek O. Effective models and the search for quantitative principles in microbial evolution. Curr Opin Microbiol 2018; 45:203-212. [PMID: 30530175 PMCID: PMC6599682 DOI: 10.1016/j.mib.2018.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/17/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Abstract
Microbes evolve rapidly. Yet they do so in idiosyncratic ways, which depend on the specific mutations that are beneficial or deleterious in a given situation. At the same time, some population-level patterns of adaptation are strikingly similar across different microbial systems, suggesting that there may also be simple, quantitative principles that unite these diverse scenarios. We review the search for simple principles in microbial evolution, ranging from the biophysical level to emergent evolutionary dynamics. A key theme has been the use of effective models, which coarse-grain over molecular and cellular details to obtain a simpler description in terms of a few effective parameters. Collectively, these theoretical approaches provide a set of quantitative principles that facilitate understanding, prediction, and potentially control of evolutionary phenomena, though formidable challenges remain due to the ecological complexity of natural populations.
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Affiliation(s)
- Benjamin H Good
- Department of Physics, University of California, Berkeley, United States; Department of Bioengineering, University of California, Berkeley, United States.
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, United States; Department of Integrative Biology, University of California, Berkeley, United States
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188
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Deatherage DE, Leon D, Rodriguez ÁE, Omar SK, Barrick JE. Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates. Nucleic Acids Res 2018; 46:9236-9250. [PMID: 30137492 PMCID: PMC6158703 DOI: 10.1093/nar/gky751] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/03/2018] [Accepted: 08/08/2018] [Indexed: 12/24/2022] Open
Abstract
Unwanted evolution of designed DNA sequences limits metabolic and genome engineering efforts. Engineered functions that are burdensome to host cells and slow their replication are rapidly inactivated by mutations, and unplanned mutations with unpredictable effects often accumulate alongside designed changes in large-scale genome editing projects. We developed a directed evolution strategy, Periodic Reselection for Evolutionarily Reliable Variants (PResERV), to discover mutations that prolong the function of a burdensome DNA sequence in an engineered organism. Here, we used PResERV to isolate Escherichia coli cells that replicate ColE1-type plasmids with higher fidelity. We found mutations in DNA polymerase I and in RNase E that reduce plasmid mutation rates by 6- to 30-fold. The PResERV method implicitly selects to maintain the growth rate of host cells, and high plasmid copy numbers and gene expression levels are maintained in some of the evolved E. coli strains, indicating that it is possible to improve the genetic stability of cellular chassis without encountering trade-offs in other desirable performance characteristics. Utilizing these new antimutator E. coli and applying PResERV to other organisms in the future promises to prevent evolutionary failures and unpredictability to provide a more stable genetic foundation for synthetic biology.
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Affiliation(s)
- Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dacia Leon
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Álvaro E Rodriguez
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Salma K Omar
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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189
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Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nat Commun 2018; 9:3796. [PMID: 30228271 PMCID: PMC6143558 DOI: 10.1038/s41467-018-06219-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 07/27/2018] [Indexed: 01/13/2023] Open
Abstract
Biological regulatory network architectures are multi-scale in their function and can adaptively acquire new functions. Gene knockout (KO) experiments provide an established experimental approach not just for studying gene function, but also for unraveling regulatory networks in which a gene and its gene product are involved. Here we study the regulatory architecture of Escherichia coli K-12 MG1655 by applying adaptive laboratory evolution (ALE) to metabolic gene KO strains. Multi-omic analysis reveal a common overall schema describing the process of adaptation whereby perturbations in metabolite concentrations lead regulatory networks to produce suboptimal states, whose function is subsequently altered and re-optimized through acquisition of mutations during ALE. These results indicate that metabolite levels, through metabolite-transcription factor interactions, have a dominant role in determining the function of a multi-scale regulatory architecture that has been molded by evolution. The function of metabolic genes in the context of regulatory networks is not well understood. Here, the authors investigate the adaptive responses of E. coli after knockout of metabolic genes and highlight the influence of metabolite levels in the evolution of regulatory function.
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190
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Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol 2018; 84:AEM.00823-18. [PMID: 30054360 DOI: 10.1128/aem.00823-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/19/2018] [Indexed: 11/20/2022] Open
Abstract
A mechanistic understanding of how new phenotypes develop to overcome the loss of a gene product provides valuable insight on both the metabolic and regulatory functions of the lost gene. The pgi gene, whose product catalyzes the second step in glycolysis, was deleted in a growth-optimized Escherichia coli K-12 MG1655 strain. The initial knockout (KO) strain exhibited an 80% drop in growth rate that was largely recovered in eight replicate, but phenotypically distinct, cultures after undergoing adaptive laboratory evolution (ALE). Multi-omic data sets showed that the loss of pgi substantially shifted pathway usage, leading to a redox and sugar phosphate stress response. These stress responses were overcome by unique combinations of innovative mutations selected for by ALE. Thus, the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after the loss of a major gene product were revealed.IMPORTANCE A mechanistic understanding of how microbes are able to overcome the loss of a gene through regulatory and metabolic changes is not well understood. Eight independent adaptive laboratory evolution (ALE) experiments with pgi knockout strains resulted in eight phenotypically distinct endpoints that were able to overcome the gene loss. Utilizing multi-omics analysis, the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after the loss of a major gene product were revealed.
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191
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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192
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Cvijović I, Nguyen Ba AN, Desai MM. Experimental Studies of Evolutionary Dynamics in Microbes. Trends Genet 2018; 34:693-703. [PMID: 30025666 PMCID: PMC6467257 DOI: 10.1016/j.tig.2018.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 11/16/2022]
Abstract
Evolutionary dynamics in laboratory microbial evolution experiments can be surprisingly complex. In the past two decades, observations of these dynamics have challenged simple models of adaptation and have shown that clonal interference, hitchhiking, ecological diversification, and contingency are widespread. In recent years, advances in high-throughput strain maintenance and phenotypic assays, the dramatically reduced cost of genome sequencing, and emerging methods for lineage barcoding have made it possible to observe evolutionary dynamics at unprecedented resolution. These new methods can now begin to provide detailed measurements of key aspects of fitness landscapes and of evolutionary outcomes across a range of systems. These measurements can highlight challenges to existing theoretical models and guide new theoretical work towards the complications that are most widely important.
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Affiliation(s)
- Ivana Cvijović
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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193
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McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol 2018; 9:1793. [PMID: 30131786 PMCID: PMC6090065 DOI: 10.3389/fmicb.2018.01793] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/17/2018] [Indexed: 11/13/2022] Open
Abstract
Adaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, new insights into the systemic function of a gene product. Two E. coli knockout strains were constructed: one that blocked the Pentose Phosphate Pathway (gnd KO) and one that decoupled the TCA cycle from electron transport (sdhCDAB KO). Despite major perturbations in central metabolism, minimal growth rate changes were found in the two knockout strains. More surprisingly, many similarities were found in their initial transcriptomic states that could be traced to similarly perturbed metabolites despite the differences in the network location of the gene perturbations and concomitant re-routing of pathway fluxes around these perturbations. However, following ALE, distinct metabolomic and transcriptomic states were realized. These included divergent flux and gene expression profiles in the gnd and sdhCDAB KOs to overcome imbalances in NADPH production and nitrogen/sulfur assimilation, respectively, that were not obvious limitations of growth in the unevolved knockouts. Therefore, this work demonstrates that ALE provides a productive approach to reveal novel insights of gene function at a systems level that cannot be found by observing the fresh knockout alone.
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Affiliation(s)
- Douglas McCloskey
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sibei Xu
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Elizabeth Brunk
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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194
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Spatial Vulnerabilities of the Escherichia coli Genome to Spontaneous Mutations Revealed with Improved Duplex Sequencing. Genetics 2018; 210:547-558. [PMID: 30076202 DOI: 10.1534/genetics.118.301345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 12/20/2022] Open
Abstract
Investigation of spontaneous mutations by next-generation sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long-term (possibly be years of) culturing, but not the freshly generated mutations that occur at very low frequencies. In this study, we established a molecularly barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 Escherichia coli cell culture samples were defined with a high confidence (P < 0.01). We also developed a hotspot-calling approach based on the run-length encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra in a single expansion process without long-term culturing.
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195
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Turner CB, Marshall CW, Cooper VS. Parallel genetic adaptation across environments differing in mode of growth or resource availability. Evol Lett 2018; 2:355-367. [PMID: 30283687 PMCID: PMC6121802 DOI: 10.1002/evl3.75] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 06/18/2018] [Accepted: 07/06/2018] [Indexed: 01/13/2023] Open
Abstract
Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here, we ask whether shared selection pressures drive parallel evolution across distinct environments. We addressed this question in experimentally evolved populations founded from a clone of the bacterium Burkholderia cenocepacia. These populations evolved for 90 days (approximately 600 generations) under all combinations of high or low carbon availability and selection for either planktonic or biofilm modes of growth. Populations that evolved in environments with shared selection pressures (either level of carbon availability or mode of growth) were more genetically similar to each other than populations from environments that shared neither characteristic. However, not all shared selection pressures led to parallel evolution. Genetic parallelism between low-carbon biofilm and low-carbon planktonic populations was very low despite shared selection for growth under low-carbon conditions, suggesting that evolution in low-carbon environments may generate stronger trade-offs between biofilm and planktonic modes of growth. For all environments, a population's fitness in a particular environment was positively correlated with the genetic similarity between that population and the populations that evolved in that particular environment. Although genetic similarity was low between low-carbon environments, overall, evolution in similar environments led to higher levels of genetic parallelism and that genetic parallelism, in turn, was correlated with fitness in a particular environment.
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Affiliation(s)
- Caroline B. Turner
- Microbiology and Molecular GeneticsUniversity of PittsburghPittsburghPennsylvania
| | | | - Vaughn S. Cooper
- Microbiology and Molecular GeneticsUniversity of PittsburghPittsburghPennsylvania
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196
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Three Substrains of the Cyanobacterium Anabaena sp. Strain PCC 7120 Display Divergence in Genomic Sequences and hetC Function. J Bacteriol 2018; 200:JB.00076-18. [PMID: 29686139 DOI: 10.1128/jb.00076-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/19/2018] [Indexed: 11/20/2022] Open
Abstract
Anabaena sp. strain PCC 7120 is a model strain for molecular studies of cell differentiation and patterning in heterocyst-forming cyanobacteria. Subtle differences in heterocyst development have been noticed in different laboratories working on the same organism. In this study, 360 mutations, including single nucleotide polymorphisms (SNPs), small insertion/deletions (indels; 1 to 3 bp), fragment deletions, and transpositions, were identified in the genomes of three substrains. Heterogeneous/heterozygous bases were also identified due to the polyploidy nature of the genome and the multicellular morphology but could be completely segregated when plated after filament fragmentation by sonication. hetC is a gene upregulated in developing cells during heterocyst formation in Anabaena sp. strain PCC 7120 and found in approximately half of other heterocyst-forming cyanobacteria. Inactivation of hetC in 3 substrains of Anabaena sp. PCC 7120 led to different phenotypes: the formation of heterocysts, differentiating cells that keep dividing, or the presence of both heterocysts and dividing differentiating cells. The expression of P hetZ -gfp in these hetC mutants also showed different patterns of green fluorescent protein (GFP) fluorescence. Thus, the function of hetC is influenced by the genomic background and epistasis and constitutes an example of evolution under way.IMPORTANCE Our knowledge about the molecular genetics of heterocyst formation, an important cell differentiation process for global N2 fixation, is mostly based on studies with Anabaena sp. strain PCC 7120. Here, we show that rapid microevolution is under way in this strain, leading to phenotypic variations for certain genes related to heterocyst development, such as hetC This study provides an example for ongoing microevolution, marked by multiple heterogeneous/heterozygous single nucleotide polymorphisms (SNPs), in a multicellular multicopy-genome microorganism.
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197
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Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng 2018; 48:82-93. [PMID: 29842925 DOI: 10.1016/j.ymben.2018.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/03/2018] [Accepted: 05/23/2018] [Indexed: 11/21/2022]
Abstract
Methylglyoxal is a highly toxic metabolite that can be produced in all living organisms. Methylglyoxal was artificially elevated by removal of the tpiA gene from a growth optimized Escherichia coli strain. The initial response to elevated methylglyoxal and its toxicity was characterized, and detoxification mechanisms were studied using adaptive laboratory evolution. We found that: 1) Multi-omics analysis revealed biological consequences of methylglyoxal toxicity, which included attack on macromolecules including DNA and RNA and perturbation of nucleotide levels; 2) Counter-intuitive cross-talk between carbon starvation and inorganic phosphate signalling was revealed in the tpiA deletion strain that required mutations in inorganic phosphate signalling mechanisms to alleviate; and 3) The split flux through lower glycolysis depleted glycolytic intermediates requiring a host of synchronized and coordinated mutations in non-intuitive network locations in order to re-adjust the metabolic flux map to achieve optimal growth. Such mutations included a systematic inactivation of the Phosphotransferase System (PTS) and alterations in cell wall biosynthesis enzyme activity. This study demonstrated that deletion of major metabolic genes followed by ALE was a productive approach to gain novel insight into the systems biology underlying optimal phenotypic states.
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198
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Lázár V, Martins A, Spohn R, Daruka L, Grézal G, Fekete G, Számel M, Jangir PK, Kintses B, Csörgő B, Nyerges Á, Györkei Á, Kincses A, Dér A, Walter FR, Deli MA, Urbán E, Hegedűs Z, Olajos G, Méhi O, Bálint B, Nagy I, Martinek TA, Papp B, Pál C. Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides. Nat Microbiol 2018; 3:718-731. [PMID: 29795541 DOI: 10.1038/s41564-018-0164-0] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 04/17/2018] [Indexed: 01/28/2023]
Abstract
Antimicrobial peptides are promising alternative antimicrobial agents. However, little is known about whether resistance to small-molecule antibiotics leads to cross-resistance (decreased sensitivity) or collateral sensitivity (increased sensitivity) to antimicrobial peptides. We systematically addressed this question by studying the susceptibilities of a comprehensive set of 60 antibiotic-resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic-resistant bacteria show a high frequency of collateral sensitivity to antimicrobial peptides, whereas cross-resistance is relatively rare. We identify clinically relevant multidrug-resistance mutations that increase bacterial sensitivity to antimicrobial peptides. Collateral sensitivity in multidrug-resistant bacteria arises partly through regulatory changes shaping the lipopolysaccharide composition of the bacterial outer membrane. These advances allow the identification of antimicrobial peptide-antibiotic combinations that enhance antibiotic activity against multidrug-resistant bacteria and slow down de novo evolution of resistance. In particular, when co-administered as an adjuvant, the antimicrobial peptide glycine-leucine-amide caused up to 30-fold decrease in the antibiotic resistance level of resistant bacteria. Our work provides guidelines for the development of efficient peptide-based therapies of antibiotic-resistant infections.
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Affiliation(s)
- Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.,Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ana Martins
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Réka Spohn
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gábor Grézal
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Mónika Számel
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Pramod K Jangir
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bálint Kintses
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ádám Györkei
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - András Kincses
- Biomolecular Electronics Research Group, Bionanoscience Unit, Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - András Dér
- Biomolecular Electronics Research Group, Bionanoscience Unit, Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Fruzsina R Walter
- Biological Barriers Research Group, Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Mária A Deli
- Biological Barriers Research Group, Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Edit Urbán
- Institute of Clinical Microbiology, Albert Szent-Györgyi Medical and Pharmaceutical Center, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsófia Hegedűs
- Institute of Pharmaceutical Analysis, University of Szeged, Szeged, Hungary
| | - Gábor Olajos
- Institute of Pharmaceutical Analysis, University of Szeged, Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | | | - István Nagy
- SeqOmics Biotechnology Ltd, Mórahalom, Hungary.,Sequencing Platform, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Tamás A Martinek
- Institute of Pharmaceutical Analysis, University of Szeged, Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
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199
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Lima WC, Pillonel T, Bertelli C, Ifrid E, Greub G, Cosson P. Genome sequencing and functional characterization of the non-pathogenic Klebsiella pneumoniae KpGe bacteria. Microbes Infect 2018; 20:293-301. [PMID: 29753816 DOI: 10.1016/j.micinf.2018.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 01/26/2023]
Abstract
Klebsiella pneumoniae is an extensively studied human pathogen responsible for a wide variety of infections. Dictyostelium discoideum is a model host organism employed to study many facets of the complex interactions between phagocytic cells and bacteria. Historically, a non-pathogenic strain of K. pneumoniae has been used to feed Dictyostelium amoebae, and more recently to study cellular mechanisms involved in bacterial recognition, ingestion and killing. Here we provide the full genome sequence and functional characterization of this non-pathogenic KpGe strain.
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Affiliation(s)
- Wanessa C Lima
- Cell Physiology and Metabolism Dpt, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland.
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, 48 rue du Bugnon, CH-1011, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University of Lausanne and University Hospital Center, 48 rue du Bugnon, CH-1011, Lausanne, Switzerland
| | - Estelle Ifrid
- Cell Physiology and Metabolism Dpt, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, 48 rue du Bugnon, CH-1011, Lausanne, Switzerland
| | - Pierre Cosson
- Cell Physiology and Metabolism Dpt, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
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200
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Steglich M, Hofmann JD, Helmecke J, Sikorski J, Spröer C, Riedel T, Bunk B, Overmann J, Neumann-Schaal M, Nübel U. Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production. Front Microbiol 2018; 9:901. [PMID: 29867812 PMCID: PMC5951980 DOI: 10.3389/fmicb.2018.00901] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
We report the frequent, convergent loss of two genes encoding the substrate-binding protein and the ATP-binding protein of an ATP-binding cassette (ABC) transporter from the genomes of unrelated Clostridioides difficile strains. This specific genomic deletion was strongly associated with the reduced uptake of tyrosine and phenylalanine and production of derived Stickland fermentation products, including p-cresol, suggesting that the affected ABC transporter had been responsible for the import of aromatic amino acids. In contrast, the transporter gene loss did not measurably affect bacterial growth or production of enterotoxins. Phylogenomic analysis of publically available genome sequences indicated that this transporter gene deletion had occurred multiple times in diverse clonal lineages of C. difficile, with a particularly high prevalence in ribotype 027 isolates, where 48 of 195 genomes (25%) were affected. The transporter gene deletion likely was facilitated by the repetitive structure of its genomic location. While at least some of the observed transporter gene deletions are likely to have occurred during the natural life cycle of C. difficile, we also provide evidence for the emergence of this mutation during long-term laboratory cultivation of reference strain R20291.
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Affiliation(s)
- Matthias Steglich
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Julia D Hofmann
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Julia Helmecke
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
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