1
|
Cai W, Liao H, Lu M, Zhou X, Cheng X, Staehelin C, Dai W. New Evolutionary Insights into RpoA: A Novel Quorum Sensing Reprograming Factor in Pseudomonas aeruginosa. Mol Biol Evol 2023; 40:msad203. [PMID: 37708386 PMCID: PMC10566545 DOI: 10.1093/molbev/msad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Abstract
Quorum-sensing (QS) coordinates the expression of virulence factors in Pseudomonas aeruginosa, an opportunistic pathogen known for causing severe infections in immunocompromised patients. QS has a master regulator, the lasR gene, but in clinical settings, P. aeruginosa isolates have been found that are QS-active but LasR-null. In this study, we developed an experimental evolutionary approach to identify additional QS-reprogramming determinants. We began the study with a LasR-null mutant with an extra copy of mexT, a transcriptional regulator gene that is known to be able to reprogram QS in laboratory LasR-null strains. In this strain, spontaneous single mexT mutations are expected to have no or little phenotypic consequences. Using this novel method, which we have named "targeted gene duplication followed by mutant screening", we identified QS-active revertants with mutations in genes other than mexT. One QS-active revertant had a point mutation in rpoA, a gene encoding the α-subunit of RNA polymerase. QS activation in this mutant was found to be associated with the downregulated expression of mexEF-oprN efflux pump genes. Our study therefore uncovers a new functional role for RpoA in regulating QS activity. Our results indicate that a RpoA-dependent regulatory circuit controlling the expression of the mexEF-oprN operon is critical for QS-reprogramming. In conclusion, our study reports on the identification of non-MexT proteins associated with QS-reprogramming in a laboratory strain, shedding light on possible QS activation mechanisms in clinical P. aeruginosa isolates.
Collapse
Affiliation(s)
- Wenjie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Huimin Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Mingqi Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Xiangting Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Xiaoyan Cheng
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| |
Collapse
|
2
|
Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nat Commun 2021; 12:5193. [PMID: 34465770 PMCID: PMC8408183 DOI: 10.1038/s41467-021-25440-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2021] [Indexed: 01/17/2023] Open
Abstract
Historical contingency and diminishing returns epistasis have been typically studied for relatively divergent genotypes and/or over long evolutionary timescales. Here, we use Saccharomyces cerevisiae to study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive mutational step. We further evolve three clones that arose under identical conditions from a common ancestor. We follow their evolutionary dynamics by lineage tracking and determine adaptive outcomes using fitness assays and whole genome sequencing. We find that diminishing returns manifests as smaller fitness gains during the 2nd step of adaptation compared to the 1st step, mainly due to a compressed distribution of fitness effects. We also find that the beneficial mutational spectra for the 2nd adaptive step are contingent on the 1st step, as we see both shared and diverging adaptive strategies. Finally, we find that adaptive loss-of-function mutations, such as nonsense and frameshift mutations, are less common in the second step of adaptation than in the first step. Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.
Collapse
|
3
|
Kinnersley M, Schwartz K, Yang DD, Sherlock G, Rosenzweig F. Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment. BMC Biol 2021; 19:20. [PMID: 33541358 PMCID: PMC7863352 DOI: 10.1186/s12915-021-00954-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/08/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Microbial evolution experiments can be used to study the tempo and dynamics of evolutionary change in asexual populations, founded from single clones and growing into large populations with multiple clonal lineages. High-throughput sequencing can be used to catalog de novo mutations as potential targets of selection, determine in which lineages they arise, and track the fates of those lineages. Here, we describe a long-term experimental evolution study to identify targets of selection and to determine when, where, and how often those targets are hit. RESULTS We experimentally evolved replicate Escherichia coli populations that originated from a mutator/nonsense suppressor ancestor under glucose limitation for between 300 and 500 generations. Whole-genome, whole-population sequencing enabled us to catalog 3346 de novo mutations that reached > 1% frequency. We sequenced the genomes of 96 clones from each population when allelic diversity was greatest in order to establish whether mutations were in the same or different lineages and to depict lineage dynamics. Operon-specific mutations that enhance glucose uptake were the first to rise to high frequency, followed by global regulatory mutations. Mutations related to energy conservation, membrane biogenesis, and mitigating the impact of nonsense mutations, both ancestral and derived, arose later. New alleles were confined to relatively few loci, with many instances of identical mutations arising independently in multiple lineages, among and within replicate populations. However, most never exceeded 10% in frequency and were at a lower frequency at the end of the experiment than at their maxima, indicating clonal interference. Many alleles mapped to key structures within the proteins that they mutated, providing insight into their functional consequences. CONCLUSIONS Overall, we find that when mutational input is increased by an ancestral defect in DNA repair, the spectrum of high-frequency beneficial mutations in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation.
Collapse
Affiliation(s)
- Margie Kinnersley
- Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA
| | - Katja Schwartz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA
| | - Dong-Dong Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.
| | - Frank Rosenzweig
- Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| |
Collapse
|
4
|
Knöppel A, Andersson DI, Näsvall J. Synonymous Mutations in rpsT Lead to Ribosomal Assembly Defects That Can Be Compensated by Mutations in fis and rpoA. Front Microbiol 2020; 11:340. [PMID: 32210939 PMCID: PMC7069363 DOI: 10.3389/fmicb.2020.00340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/17/2020] [Indexed: 11/21/2022] Open
Abstract
We previously described how four deleterious synonymous mutations in the Salmonella enterica rpsT gene (encoding ribosomal protein S20) result in low S20 levels that can be compensated by mutations that restore [S20]. Here, we have further studied the cause for the deleterious effects of S20 deficiency and found that the S20 mutants were also deficient in four other 30S proteins (S1, S2, S12, and S21), which is likely due to an assembly defect of the S20 deficient 30S subunits. We examined the compensatory effect by six additional mutations affecting the global regulator Fis and the C-terminal domain of the α subunit of RNA polymerase (encoded by rpoA). The fis and rpoA mutations restored the S20 levels, concomitantly restoring the assembly defect and the levels of S1, S2, S12, and S21. These results illustrate the complexity of compensatory evolution and how the negative effects of deleterious mutations can be suppressed by a multitude of mechanisms. Additionally, we found that the mutations in fis and rpoA caused reduced expression of other ribosomal components. Notably, some of the fis mutations and the rpoA mutation corrected the fitness of the rpsT mutants to wild-type levels, although expression of other ribosomal components was reduced compared to wild-type. This finding raises new questions regarding the relation between translation capacity and growth rate.
Collapse
|
5
|
Blount ZD, Lenski RE, Losos JB. Contingency and determinism in evolution: Replaying life’s tape. Science 2018; 362:362/6415/eaam5979. [DOI: 10.1126/science.aam5979] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Historical processes display some degree of “contingency,” meaning their outcomes are sensitive to seemingly inconsequential events that can fundamentally change the future. Contingency is what makes historical outcomes unpredictable. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by the deterministic force of natural selection, but natural selection works upon variation that arises unpredictably through time by random mutation, and even beneficial mutations can be lost by chance through genetic drift. Moreover, evolution has taken place within a planetary environment with a particular history of its own. This tension between determinism and contingency makes evolutionary biology a kind of hybrid between science and history. While philosophers of science examine the nuances of contingency, biologists have performed many empirical studies of evolutionary repeatability and contingency. Here, we review the experimental and comparative evidence from these studies. Replicate populations in evolutionary “replay” experiments often show parallel changes, especially in overall performance, although idiosyncratic outcomes show that the particulars of a lineage’s history can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. Ongoing research on the structure of adaptive landscapes is providing additional insight into the interplay of fate and chance in the evolutionary process.
Collapse
Affiliation(s)
- Zachary D. Blount
- Department of Microbiology and Molecular Genetics and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
- Department of Biology, Kenyon College, Gambier, OH 43022, USA
| | - Richard E. Lenski
- Department of Microbiology and Molecular Genetics and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Jonathan B. Losos
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| |
Collapse
|
6
|
Knöppel A, Knopp M, Albrecht LM, Lundin E, Lustig U, Näsvall J, Andersson DI. Genetic Adaptation to Growth Under Laboratory Conditions in Escherichia coli and Salmonella enterica. Front Microbiol 2018; 9:756. [PMID: 29755424 PMCID: PMC5933015 DOI: 10.3389/fmicb.2018.00756] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/04/2018] [Indexed: 11/16/2022] Open
Abstract
Experimental evolution under controlled laboratory conditions is becoming increasingly important to address various evolutionary questions, including, for example, the dynamics and mechanisms of genetic adaptation to different growth and stress conditions. In such experiments, mutations typically appear that increase the fitness under the conditions tested (medium adaptation), but that are not necessarily of interest for the specific research question. Here, we have identified mutations that appeared during serial passage of E. coli and S. enterica in four different and commonly used laboratory media and measured the relative competitive fitness and maximum growth rate of 111 genetically re-constituted strains, carrying different single and multiple mutations. Little overlap was found between the mutations that were selected in the two species and the different media, implying that adaptation occurs via different genetic pathways. Furthermore, we show that commonly occurring adaptive mutations can generate undesired genetic variation in a population and reduce the accuracy of competition experiments. However, by introducing media adaptation mutations with large effects into the parental strain that was used for the evolution experiment, the variation (standard deviation) was decreased 10-fold, and it was possible to measure fitness differences between two competitors as small as |s| < 0.001.
Collapse
Affiliation(s)
- Anna Knöppel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michael Knopp
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lisa M Albrecht
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Lundin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ulrika Lustig
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
7
|
González-González A, Hug SM, Rodríguez-Verdugo A, Patel JS, Gaut BS. Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression. Mol Biol Evol 2017; 34:2839-2855. [PMID: 28961910 PMCID: PMC5815632 DOI: 10.1093/molbev/msx216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerous E. coli evolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2 °C. Among the eight mutations, two rho mutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of ∼20%. The rpoB mutations affected the expression of ∼1,700 genes; rho mutations affected the expression of fewer genes but most (83%) were a subset of those altered by rpoB mutants. Across the eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0 °C state. The beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, but they caused parallel phenotypic effects on gene expression and genome-wide transcriptional termination.
Collapse
Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Shaun M. Hug
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
| | - Alejandra Rodríguez-Verdugo
- Department of Environmental Systems Sciences, ETH Zürich, Zürich,
Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf,
Switzerland
| | | | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
| |
Collapse
|
8
|
Marchal M, Goldschmidt F, Derksen-Müller SN, Panke S, Ackermann M, Johnson DR. A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations. BMC Evol Biol 2017; 17:106. [PMID: 28438135 PMCID: PMC5402672 DOI: 10.1186/s12862-017-0950-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 04/04/2017] [Indexed: 12/02/2022] Open
Abstract
Background While mutualistic interactions between different genotypes are pervasive in nature, their evolutionary origin is not clear. The dilemma is that, for mutualistic interactions to emerge and persist, an investment into the partner genotype must pay off: individuals of a first genotype that invest resources to promote the growth of a second genotype must receive a benefit that is not equally accessible to individuals that do not invest. One way for exclusive benefits to emerge is through spatial structure (i.e., physical barriers to the movement of individuals and resources). Results Here we propose that organisms can evolve their own spatial structure based on physical attachment between individuals, and we hypothesize that attachment evolves when spatial proximity to members of another species is advantageous. We tested this hypothesis using experimental evolution with combinations of E. coli strains that depend on each other to grow. We found that attachment between cells repeatedly evolved within 8 weeks of evolution and observed that many different types of mutations potentially contributed to increased attachment. Conclusions We postulate a general principle by which passive beneficial interactions between organisms select for attachment, and attachment then provides spatial structure that could be conducive for the evolution of active mutualistic interactions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0950-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marie Marchal
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Felix Goldschmidt
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Selina N Derksen-Müller
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Martin Ackermann
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland. .,Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland.
| | - David R Johnson
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland.
| |
Collapse
|
9
|
Zatoń-Dobrowolska M, Moska M, Mucha A, Wierzbicki H, Przysiecki P, Dobrowolski M. Variation in fur farm and wild populations of the red fox, Vulpes vulpes (Carnivora: Canidae) — Part I: Morphometry. CANADIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1139/cjas-2016-0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This paper demonstrates the influence of artificial selection on morphometric traits in the red fox [Vulpes vulpes (Linnaeus, 1758)]. Measurements and two proportion coefficients were analysed in 132 wild and 199 farm red foxes. The two groups differed significantly (P ≤ 0.05) on all but one of the measurements. Eight out of 11 measurements were significantly greater in the farm fox population, while only tail length, ear height, and length of the right hind limb were greater in the population of wild foxes. The opposite trend was observed when analysing variation in the measurements — the farm foxes were characterized by a greater variability only in the case of body weight, body length, and breadth of chest. When analysing the sexual dimorphism index in different sex and population groups, in almost all analysed traits, the greatest differences occurred between farm males and wild females. All of the traits examined in this study are important for survival of wild foxes. However, because importance of some traits was reduced during domestication and selective breeding (farm foxes do not have to fight for survival), the genetic relationship between them may have weakened. Other possible causes of morphological differences between the studied groups of red foxes are discussed as well.
Collapse
Affiliation(s)
| | - Magdalena Moska
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 51-631 Wroclaw, Poland
| | - Anna Mucha
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 51-631 Wroclaw, Poland
| | - Heliodor Wierzbicki
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 51-631 Wroclaw, Poland
| | - Piotr Przysiecki
- Institute of Agriculture, State School of Higher Education, 64-100 Leszno, Poland
| | - Maciej Dobrowolski
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
| |
Collapse
|
10
|
Lescat M, Launay A, Ghalayini M, Magnan M, Glodt J, Pintard C, Dion S, Denamur E, Tenaillon O. Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut. Mol Ecol 2016; 26:1802-1817. [PMID: 27661780 DOI: 10.1111/mec.13851] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023]
Abstract
Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
Collapse
Affiliation(s)
- Mathilde Lescat
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Paris, France
| | - Adrien Launay
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mohamed Ghalayini
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France
| | - Mélanie Magnan
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jérémy Glodt
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Coralie Pintard
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sara Dion
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Nord Val de Seine, Paris, France
| | - Olivier Tenaillon
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
11
|
Plucain J, Suau A, Cruveiller S, Médigue C, Schneider D, Le Gac M. Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria. BMC Evol Biol 2016; 16:86. [PMID: 27108090 PMCID: PMC4841947 DOI: 10.1186/s12862-016-0662-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The impact of historical contingency, i.e. the past evolutionary history of a population, on further adaptation is mostly unknown at both the phenotypic and genomic levels. We addressed this question using a two-step evolution experiment. First, replicate populations of Escherichia coli were propagated in four different environmental conditions for 1000 generations. Then, all replicate populations were transferred and propagated for further 1000 generations to a single new environment. RESULTS Using this two-step experimental evolution strategy, we investigated, at both the phenotypic and genomic levels, whether and how adaptation in the initial historical environments impacted evolutionary trajectories in a new environment. We showed that both the growth rate and fitness of the evolved populations obtained after the second step of evolution were contingent upon past evolutionary history. In contrast however, the genes that were modified during the second step of evolution were independent from the previous history of the populations. CONCLUSIONS Our work suggests that historical contingency affects phenotypic adaptation to a new environment. This was however not reflected at the genomic level implying complex relationships between environmental factors and the genotype-to-phenotype map.
Collapse
Affiliation(s)
- Jessica Plucain
- Univ. Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications (TIMC-IMAG), F-38000, Grenoble, France.,Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, F-38000, Grenoble, France
| | - Antonia Suau
- Univ. Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications (TIMC-IMAG), F-38000, Grenoble, France.,Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, F-38000, Grenoble, France.,Conservatoire national des arts et métiers, Paris, France
| | - Stéphane Cruveiller
- Direction des Sciences du Vivant, CEA, Institut de Génomique, Genoscope & CNRS-UMR8030, Évry, France.,Laboratoire d'Analyses Bioinformatiques en Génomique et Métabolisme, Évry, France
| | - Claudine Médigue
- Direction des Sciences du Vivant, CEA, Institut de Génomique, Genoscope & CNRS-UMR8030, Évry, France.,Laboratoire d'Analyses Bioinformatiques en Génomique et Métabolisme, Évry, France
| | - Dominique Schneider
- Univ. Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications (TIMC-IMAG), F-38000, Grenoble, France.,Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, F-38000, Grenoble, France
| | - Mickaël Le Gac
- Univ. Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications (TIMC-IMAG), F-38000, Grenoble, France. .,Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, F-38000, Grenoble, France. .,Ifremer, DYNECO/Pelagos, 29280, Plouzané, France.
| |
Collapse
|
12
|
Ying BW, Matsumoto Y, Kitahara K, Suzuki S, Ono N, Furusawa C, Kishimoto T, Yomo T. Bacterial transcriptome reorganization in thermal adaptive evolution. BMC Genomics 2015; 16:802. [PMID: 26474851 PMCID: PMC4609109 DOI: 10.1186/s12864-015-1999-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/03/2015] [Indexed: 11/30/2022] Open
Abstract
Background Evolution optimizes a living system at both the genome and transcriptome levels. Few studies have investigated transcriptome evolution, whereas many studies have explored genome evolution in experimentally evolved cells. However, a comprehensive understanding of evolutionary mechanisms requires knowledge of how evolution shapes gene expression. Here, we analyzed Escherichia coli strains acquired during long-term thermal adaptive evolution. Results Evolved and ancestor Escherichia coli cells were exponentially grown under normal and high temperatures for subsequent transcriptome analysis. We found that both the ancestor and evolved cells had comparable magnitudes of transcriptional change in response to heat shock, although the evolutionary progression of their expression patterns during exponential growth was different at either normal or high temperatures. We also identified inverse transcriptional changes that were mediated by differences in growth temperatures and genotypes, as well as negative epistasis between genotype—and heat shock-induced transcriptional changes. Principal component analysis revealed that transcriptome evolution neither approached the responsive state at the high temperature nor returned to the steady state at the regular temperature. We propose that the molecular mechanisms of thermal adaptive evolution involve the optimization of steady-state transcriptomes at high temperatures without disturbing the heat shock response. Conclusions Our results suggest that transcriptome evolution works to maintain steady-state gene expression during constrained differentiation at various evolutionary stages, while also maintaining responsiveness to environmental stimuli and transcriptome homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1999-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bei-Wen Ying
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan.
| | - Yuki Matsumoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan. .,Present address: IMS, RIKEN, Kanagawa, 230-0045, Japan.
| | - Kazuki Kitahara
- Graduate School of Information Science and Technology, Osaka University, Osaka, 565-0871, Japan.
| | | | - Naoaki Ono
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Chikara Furusawa
- Graduate School of Information Science and Technology, Osaka University, Osaka, 565-0871, Japan. .,QBiC, RIKEN, Osaka, 565-0874, Japan.
| | | | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, Osaka, 565-0871, Japan. .,Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan. .,Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Tokyo, 102-0076, Japan.
| |
Collapse
|
13
|
Marchetti M, Jauneau A, Capela D, Remigi P, Gris C, Batut J, Masson-Boivin C. Shaping bacterial symbiosis with legumes by experimental evolution. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:956-964. [PMID: 25105803 DOI: 10.1094/mpmi-03-14-0083-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta-in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.
Collapse
|
14
|
Guo Y, Li Y, Su L, Chang D, Liu W, Wang T, Yuan Y, Fang X, Wang J, Li T, Fang C, Dai W, Liu C. Comparative genomic analysis of Klebsiella pneumonia (LCT-KP214) and a mutant strain (LCT-KP289) obtained after spaceflight. BMC Genomics 2014; 15:589. [PMID: 25015528 PMCID: PMC4226956 DOI: 10.1186/1471-2164-15-589] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 07/07/2014] [Indexed: 01/07/2023] Open
Abstract
Background With the development of space science, it is important to analyze the relationship between the space environment and genome variations that might cause phenotypic changes in microbes. Klebsiella pneumoniae is commonly found on the human body and is resistant to multiple drugs. To study space-environment-induced genome variations and drug resistance changes, K. pneumoniae was carried into outer space by the Shenzhou VIII spacecraft. Results The K. pneumoniae strain LCT-KP289 was selected after spaceflight based on its phenotypic differences compared to the ground-control strain. Analysis of genomic structural variations revealed one inversion, 25 deletions, fifty-nine insertions, two translocations and six translocations with inversions. In addition, 155 and 400 unique genes were observed in LCT-KP214 and LCT-KP289, respectively, including the gene encoding dihydroxyacetone kinase, which generates the ATP and NADH required for microbial growth. Furthermore, a large number of mutant genes were related to transport and metabolism. Phylogenetic analysis revealed that most genes in these two strains had a dN/dS value greater than 1, indicating that the strain diversity increased after spaceflight. Analysis of drug-resistance phenotypes revealed that the K. pneumoniae strain LCT-KP289 was resistant to sulfamethoxazole, whereas the control strain, LCT-KP214, was not; both strains were resistant to benzylpenicillin, ampicillin, lincomycin, vancomycin, chloramphenicol and streptomycin. The sulfamethoxazole resistance may be associated with sequences in Scaffold7 in LCT-KP289, which were not observed in LCT-K214; this scaffold contained the gene sul1. In the strain LCT-KP289, we also observed a drug-resistance integron containing emrE (confers multidrug resistance) and ant (confers resistance to spectinomycin, streptomycin, tobramycin, kanamycin, sisomicin, dibekacin, and gentamicin). The gene ampC (confers resistance to penicillin, cephalosporin-ii and cephalosporin-i) was present near the integron. In addition, 30 and 26 drug-resistance genes were observed in LCT-KP289 and LCT-KP214, respectively. Conclusions Comparison of a K. pneumoniae strain obtained after spaceflight with the ground-control strain revealed genome variations and phenotypic changes and elucidated the genomic basis of the acquired drug resistance. These data pave the way for future studies on the effects of spaceflight.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Wenkui Dai
- Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, Beijing 100853, China.
| | | |
Collapse
|