1
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Jiao J, Lv X, Shen C, Morigen M. Genome and transcriptomic analysis of the adaptation of Escherichia coli to environmental stresses. Comput Struct Biotechnol J 2024; 23:2132-2140. [PMID: 38817967 PMCID: PMC11137339 DOI: 10.1016/j.csbj.2024.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/05/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
In natural niches, bacteria are forced to spend most of their lives under various environmental stresses, such as nutrient limitation, heavy metal pollution, heat and antibiotic stress. To cope with adverse environments, bacterial genome can during the life cycle, produce potential adaptive mutants. The genomic changes, especially mutations, in the genes that encode RNA polymerase and transcription factors, might lead to variations in the transcriptome. These variations enable bacteria to cope with environmental stresses through physiological adaptation in response to stress. This paper reviews the recent contributions of genomic and transcriptomic analyses in understanding the adaption mechanism of Escherichia coli to environmental stresses. Various genomic changes have been observed in E. coli strains in laboratory or under natural stresses, including starvation, heavy metals, acidic conditions, heat shock and antibiotics. The mutations include slight changes (one to several nucleotides), deletions, insertions, chromosomal rearrangements and variations in copy numbers. The transcriptome of E. coli largely changes due to genomic mutations. However, the transcriptional profiles vary due to variations in stress selections. Cellular adaptation to the selections is associated with transcriptional changes resulting from genomic mutations. Changes in genome and transcriptome are cooperative and jointly affect the adaptation of E. coli to different environments. This comprehensive review reveals that coordination of genome mutations and transcriptional variations needs to be explored further to provide a better understanding of the mechanisms of bacterial adaptation to stresses.
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Affiliation(s)
- Jianlu Jiao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xiaoli Lv
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chongjie Shen
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Morigen Morigen
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot, China
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2
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Fan D, Liu L, Yuen B, Sun L, Fu Y, Liu Y, Liao R, Qu Y, Liu C, Zhou Q. An Additional L451G452N453 in the RpoB Protein Suppressed the Synthetic Lethality in Escherichia coli at 37 Degrees Caused by Depletion of DnaK/J and Trigger Factor. J Basic Microbiol 2024:e2400253. [PMID: 39286860 DOI: 10.1002/jobm.202400253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/16/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024]
Abstract
Escherichia coli depletion of chaperone trigger factor and DnaK/J were not viable at 37°C, but viable below 30°C. Among the engineered E. coli depleted of trigger factor and DnaK/J, one strain Z625, exhibited survival at 37°C, while another strain Z629 only survived below 30°C. Comparative analysis of fatty acid profiles of Z625 and Z629 revealed absence of numerous saturated fatty acids in Z625 as compared to the wild-type E. coli BW25113. In addition, increased unsaturated fatty acids were present in Z625, whereas the fatty acids profile of Z629 closely resembled that of BW25113. Whole genome sequencing revealed a 9-bp insertion in rpoB of Z625. Combined structural analysis of simulated RpoB protein bearing the amino acid sequence L451G452N453 insertion and susceptibility analysis to rifampicin suggested that the insertion did not disturb the individual RpoB structure as beta subunit of RNA polymerase. Comparative transcriptomic analysis of Z625 and Z629 suggested that this insertion impacted transcription of the overall RNA polymerase in Z625, leading to potential repression of some genes whose overexpression was toxic to E. coli. Additionally, Z625 exhibited distinctive metabolic adaptations, likely contributing to its survival at 37°C. In summary, our study elucidated one LGN insertion in rpoB that impacts transcriptional regulation in E. coli, thereby explaining the survival of E. coli depletion of trigger factor and DnaK/J at 37°C, and these founding suggested that some simple mutations in critical genes like rpoB might play an important role in driving adaptive evolution.
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Affiliation(s)
- Dongjie Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lushan Liu
- Emergency Department of China Rehabilitation Research Center, Fengtai District, Capital Medical University, Beijing, China
| | - Bella Yuen
- Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada
| | - Lu Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuliang Fu
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Yan Liu
- Peking University Health Science Center, Beijing, China
| | - Rui Liao
- Beijing Best HealthCare Medical Technology Co. Ltd., Economic and Technological Development Area, Beijing, China
| | - Yanli Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Qiming Zhou
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Economic and Technological Development Area, Beijing, China
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González-González A, Batarseh TN, Rodríguez-Verdugo A, Gaut BS. Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the rho and rpoB Genes of Escherichia coli during High-Temperature Adaptation. Mol Biol Evol 2024; 41:msae187. [PMID: 39235107 DOI: 10.1093/molbev/msae187] [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: 05/12/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Epistasis is caused by genetic interactions among mutations that affect fitness. To characterize properties and potential mechanisms of epistasis, we engineered eight double mutants that combined mutations from the rho and rpoB genes of Escherichia coli. The two genes encode essential functions for transcription, and the mutations in each gene were chosen because they were beneficial for adaptation to thermal stress (42.2 °C). The double mutants exhibited patterns of fitness epistasis that included diminishing returns epistasis at 42.2 °C, stronger diminishing returns between mutations with larger beneficial effects and both negative and positive (sign) epistasis across environments (20.0 °C and 37.0 °C). By assessing gene expression between single and double mutants, we detected hundreds of genes with gene expression epistasis. Previous work postulated that highly connected hub genes in coexpression networks have low epistasis, but we found the opposite: hub genes had high epistasis values in both coexpression and protein-protein interaction networks. We hypothesized that elevated epistasis in hub genes reflected that they were enriched for targets of Rho termination but that was not the case. Altogether, gene expression and coexpression analyses revealed that thermal adaptation occurred in modules, through modulation of ribonucleotide biosynthetic processes and ribosome assembly, the attenuation of expression in genes related to heat shock and stress responses, and with an overall trend toward restoring gene expression toward the unstressed state.
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Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Tiffany N Batarseh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
| | | | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
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4
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Santos MA, Carromeu-Santos A, Quina AS, Antunes MA, Kristensen TN, Santos M, Matos M, Fragata I, Simões P. Experimental Evolution in a Warming World: The Omics Era. Mol Biol Evol 2024; 41:msae148. [PMID: 39034684 PMCID: PMC11331425 DOI: 10.1093/molbev/msae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
A comprehensive understanding of the genetic mechanisms that shape species responses to thermal variation is essential for more accurate predictions of the impacts of climate change on biodiversity. Experimental evolution with high-throughput resequencing approaches (evolve and resequence) is a highly effective tool that has been increasingly employed to elucidate the genetic basis of adaptation. The number of thermal evolve and resequence studies is rising, yet there is a dearth of efforts to integrate this new wealth of knowledge. Here, we review this literature showing how these studies have contributed to increase our understanding on the genetic basis of thermal adaptation. We identify two major trends: highly polygenic basis of thermal adaptation and general lack of consistency in candidate targets of selection between studies. These findings indicate that the adaptive responses to specific environments are rather independent. A review of the literature reveals several gaps in the existing research. Firstly, there is a paucity of studies done with organisms of diverse taxa. Secondly, there is a need to apply more dynamic and ecologically relevant thermal environments. Thirdly, there is a lack of studies that integrate genomic changes with changes in life history and behavioral traits. Addressing these issues would allow a more in-depth understanding of the relationship between genotype and phenotype. We highlight key methodological aspects that can address some of the limitations and omissions identified. These include the need for greater standardization of methodologies and the utilization of new technologies focusing on the integration of genomic and phenotypic variation in the context of thermal adaptation.
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Affiliation(s)
- Marta A Santos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carromeu-Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S Quina
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Almada, Portugal
| | - Marta A Antunes
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Mauro Santos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GBBE), Universitat Autonòma de Barcelona, Bellaterra, Spain
| | - Margarida Matos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Fragata
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Venkataraman P, Nagendra P, Ahlawat N, Brajesh RG, Saini S. Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence. Front Mol Biosci 2024; 11:1286824. [PMID: 38660375 PMCID: PMC11039892 DOI: 10.3389/fmolb.2024.1286824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/15/2024] [Indexed: 04/26/2024] Open
Abstract
Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.
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Affiliation(s)
| | | | | | | | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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6
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Sanders BR, Miller JE, Ahmidouch N, Graves JL, Thomas MD. Genotype-by-environment interactions govern fitness changes associated with adaptive mutations in two-component response systems. Front Genet 2024; 15:1349507. [PMID: 38463171 PMCID: PMC10920338 DOI: 10.3389/fgene.2024.1349507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction: Two-component response systems (TCRS) are the main mechanism by which prokaryotes acclimate to changing environments. These systems are composed of a membrane bound histidine kinase (HK) that senses external signals and a response regulator (RR) that activates transcription of response genes. Despite their known role in acclimation, little is known about the role TCRS play in environmental adaptation. Several experimental evolution studies have shown the acquisition of mutations in TCRS during adaptation, therefore here we set out to characterize the adaptive mechanism resulting from these mutations and evaluate whether single nucleotide changes in one gene could induce variable genotype-by-environment (GxE) interactions. Methods: To do this, we assessed fitness changes and differential gene expression for four adaptive mutations in cusS, the gene that encodes the HK CusS, acquired by Escherichia coli during silver adaptation. Results: Fitness assays showed that as the environment changed, each mutant displayed a unique fitness profile with greatest fitness in the original selection environment. RNAseq then indicated that, in ± silver nitrate, each mutant induces a primary response that upregulates cusS, its RR cusR, and constitutively expresses the target response genes cusCFBA. This then induces a secondary response via differential expression of genes regulated by the CusR through TCRS crosstalk. Finally, each mutant undergoes fitness tuning through unique tertiary responses that result in gene expression patterns specific for the genotype, the environment and optimized for the original selection conditions. Discussion: This three-step response shows that different mutations in a single gene leads to individualized phenotypes governed by unique GxE interactions that not only contribute to transcriptional divergence but also to phenotypic plasticity.
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Affiliation(s)
| | | | | | | | - Misty D. Thomas
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
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7
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Abstract
Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.
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Affiliation(s)
- María Mercedes Zambrano
- Corpogen Research Center, Bogotá, Colombia;
- Dirección de Investigaciones y Transferencia de Conocimiento, Universidad Central, Bogotá, Colombia
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8
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Liang J, Cameron G, Faucher SP. Development of heat-shock resistance in Legionella pneumophila modeled by experimental evolution. Appl Environ Microbiol 2023; 89:e0066623. [PMID: 37668382 PMCID: PMC10537758 DOI: 10.1128/aem.00666-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/29/2023] [Indexed: 09/06/2023] Open
Abstract
Because it can grow in buildings with complex hot water distribution systems (HWDS), healthcare facilities recognize the waterborne bacterium Legionella pneumophila as a major nosocomial infection threat and often try to clear the systems with a pasteurization process known as superheat-and-flush. After this treatment, many facilities find that the contaminating populations slowly recover, suggesting the possibility of in situ evolution favoring increased survival in high-temperature conditions. To mimic this process in a controlled environment, an adaptive laboratory evolution model was used to select a wild-type strain of L. pneumophila for survival to transient exposures to temperatures characteristic of routine hot water use or failed pasteurization processes in HWDS. Over their evolution, these populations became insensitive to exposure to 55°C and developed the ability to survive short exposures to 59°C heat shock. Heat-adapted lineages maintained a higher expression of heat-shock genes during low-temperature incubation in freshwater, suggesting a pre-adaptation to heat stress. Although there were distinct mutation profiles in each of the heat-adapted lineages, each acquired multiple mutations in the DnaJ/DnaK/ClpB disaggregase complex, as well as mutations in chaperone htpG and protease clpX. These mutations were specific to heat-shock survival and were not seen in control lineages included in the experimental model without exposure to heat shock. This study supports in situ observations of adaptation to heat stress and demonstrates the potential of L. pneumophila to develop resistance to control measures. IMPORTANCE As a bacterium that thrives in warm water ecosystems, Legionella pneumophila is a key factor motivating regulations on hot water systems. Two major measures to control Legionella are high circulating temperatures intended to curtail growth and the use of superheat-and-flush pasteurization processes to eliminate established populations. Facilities often suffer recolonization of their hot water systems; hospitals are particularly at risk due to the severe nosocomial pneumoniae caused by Legionella. To understand these long-term survivors, we have used an adaptive laboratory evolution model to replicate this process. We find major differences between the mutational profiles of heat-adapted and heat-naïve L. pneumophila populations including mutations in major heat-shock genes like chaperones and proteases. This model demonstrates that well-validated treatment protocols are needed to clear contaminated systems and-in an analog to antibiotic resistance-the importance of complete eradication of the resident population to prevent selection for more persistent bacteria.
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Affiliation(s)
- Jeffrey Liang
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Gillian Cameron
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Sébastien P. Faucher
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
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Kelbrick M, Hesse E, O' Brien S. Cultivating antimicrobial resistance: how intensive agriculture ploughs the way for antibiotic resistance. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001384. [PMID: 37606636 PMCID: PMC10482381 DOI: 10.1099/mic.0.001384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
Antimicrobial resistance (AMR) is a growing threat to public health, global food security and animal welfare. Despite efforts in antibiotic stewardship, AMR continues to rise worldwide. Anthropogenic activities, particularly intensive agriculture, play an integral role in the dissemination of AMR genes within natural microbial communities - which current antibiotic stewardship typically overlooks. In this review, we examine the impact of anthropogenically induced temperature fluctuations, increased soil salinity, soil fertility loss, and contaminants such as metals and pesticides on the de novo evolution and dissemination of AMR in the environment. These stressors can select for AMR - even in the absence of antibiotics - via mechanisms such as cross-resistance, co-resistance and co-regulation. Moreover, anthropogenic stressors can prime bacterial physiology against stress, potentially widening the window of opportunity for the de novo evolution of AMR. However, research to date is typically limited to the study of single isolated bacterial species - we lack data on how intensive agricultural practices drive AMR over evolutionary timescales in more complex microbial communities. Furthermore, a multidisciplinary approach to fighting AMR is urgently needed, as it is clear that the drivers of AMR extend far beyond the clinical environment.
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Affiliation(s)
- Matthew Kelbrick
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Elze Hesse
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Siobhán O' Brien
- Department of Microbiology, Moyne Institute for Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Republic of Ireland
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Ghenu AH, Amado A, Gordo I, Bank C. Epistasis decreases with increasing antibiotic pressure but not temperature. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220058. [PMID: 37004727 PMCID: PMC10067269 DOI: 10.1098/rstb.2022.0058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Predicting mutational effects is essential for the control of antibiotic resistance (ABR). Predictions are difficult when there are strong genotype-by-environment (G × E), gene-by-gene (G × G or epistatic) or gene-by-gene-by-environment (G × G × E) interactions. We quantified G × G × E effects in Escherichia coli across environmental gradients. We created intergenic fitness landscapes using gene knock-outs and single-nucleotide ABR mutations previously identified to vary in the extent of G × E effects in our environments of interest. Then, we measured competitive fitness across a complete combinatorial set of temperature and antibiotic dosage gradients. In this way, we assessed the predictability of 15 fitness landscapes across 12 different but related environments. We found G × G interactions and rugged fitness landscapes in the absence of antibiotic, but as antibiotic concentration increased, the fitness effects of ABR genotypes quickly overshadowed those of gene knock-outs, and the landscapes became smoother. Our work reiterates that some single mutants, like those conferring resistance or susceptibility to antibiotics, have consistent effects across genetic backgrounds in stressful environments. Thus, although epistasis may reduce the predictability of evolution in benign environments, evolution may be more predictable in adverse environments. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Ana-Hermina Ghenu
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - André Amado
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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11
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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. RESEARCH SQUARE 2023:rs.3.rs-2729651. [PMID: 37090546 PMCID: PMC10120744 DOI: 10.21203/rs.3.rs-2729651/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced twelve RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations resulted in large shifts in the fear vs. greed tradeoff, likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that often have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species. The results suggest that the fear vs. greed tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.
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Affiliation(s)
- Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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12
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McGuire BE, Nano FE. Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains. BMC Genomics 2023; 24:154. [PMID: 36973666 PMCID: PMC10044804 DOI: 10.1186/s12864-023-09266-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND High temperatures cause a suite of problems for cells, including protein unfolding and aggregation; increased membrane fluidity; and changes in DNA supercoiling, RNA stability, transcription and translation. Consequently, enhanced thermotolerance can evolve through an unknown number of genetic mechanisms even in the simple model bacterium Escherichia coli. To date, each E. coli study exploring this question resulted in a different set of mutations. To understand the changes that can arise when an organism evolves to grow at higher temperatures, we sequenced and analyzed two previously described E. coli strains, BM28 and BM28 ΔlysU, that have been laboratory adapted to the highest E. coli growth temperature reported to date. RESULTS We found three large deletions in the BM28 and BM28 ΔlysU strains of 123, 15 and 8.5 kb in length and an expansion of IS10 elements. We found that BM28 and BM28 ΔlysU have considerably different genomes, suggesting that the BM28 culture that gave rise to BM28 and BM28 ΔlysU was a mixed population of genetically different cells. Consistent with published findings of high GroESL expression in BM28, we found that BM28 inexplicitly carries the groESL bearing plasmid pOF39 that was maintained simply by high-temperature selection pressure. We identified over 200 smaller insertions, deletions, single nucleotide polymorphisms and other mutations, including changes in master regulators such as the RNA polymerase and the transcriptional termination factor Rho. Importantly, this genome analysis demonstrates that the commonly cited findings that LysU plays a crucial role in thermotolerance and that GroESL hyper-expression is brought about by chromosomal mutations are based on a previous misinterpretation of the genotype of BM28. CONCLUSIONS This whole-genome sequencing study describes genetically distinct mechanisms of thermotolerance evolution from those found in other heat-evolved E. coli strains. Studying adaptive laboratory evolution to heat in simple model organisms is important in the context of climate change. It is important to better understand genetic mechanisms of enhancing thermotolerance in bacteria and other organisms, both in terms of optimizing laboratory evolution methods for various organisms and in terms of potential genetic engineering of organisms most at risk or most important to our societies and ecosystems.
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Affiliation(s)
- Bailey E McGuire
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada.
| | - Francis E Nano
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada
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13
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Alkim C, Farias D, Fredonnet J, Serrano-Bataille H, Herviou P, Picot M, Slama N, Dejean S, Morin N, Enjalbert B, François JM. Toxic effect and inability of L-homoserine to be a nitrogen source for growth of Escherichia coli resolved by a combination of in vivo evolution engineering and omics analyses. Front Microbiol 2022; 13:1051425. [PMID: 36583047 PMCID: PMC9792984 DOI: 10.3389/fmicb.2022.1051425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
L-homoserine is a pivotal intermediate in the carbon and nitrogen metabolism of E. coli. However, this non-canonical amino acid cannot be used as a nitrogen source for growth. Furthermore, growth of this bacterium in a synthetic media is potently inhibited by L-homoserine. To understand this dual effect, an adapted laboratory evolution (ALE) was applied, which allowed the isolation of a strain able to grow with L-homoserine as the nitrogen source and was, at the same time, desensitized to growth inhibition by this amino acid. Sequencing of this evolved strain identified only four genomic modifications, including a 49 bp truncation starting from the stop codon of thrL. This mutation resulted in a modified thrL locus carrying a thrL* allele encoding a polypeptide 9 amino acids longer than the thrL encoded leader peptide. Remarkably, the replacement of thrL with thrL* in the original strain MG1655 alleviated L-homoserine inhibition to the same extent as strain 4E, but did not allow growth with this amino acid as a nitrogen source. The loss of L-homoserine toxic effect could be explained by the rapid conversion of L-homoserine into threonine via the thrL*-dependent transcriptional activation of the threonine operon thrABC. On the other hand, the growth of E. coli on a mineral medium with L-homoserine required an activation of the threonine degradation pathway II and glycine cleavage system, resulting in the release of ammonium ions that were likely recaptured by NAD(P)-dependent glutamate dehydrogenase. To infer about the direct molecular targets of L-homoserine toxicity, a transcriptomic analysis of wild-type MG1655 in the presence of 10 mM L-homoserine was performed, which notably identified a potent repression of locomotion-motility-chemotaxis process and of branched-chain amino acids synthesis. Since the magnitude of these effects was lower in a ΔthrL mutant, concomitant with a twofold lower sensitivity of this mutant to L-homoserine, it could be argued that growth inhibition by L-homoserine is due to the repression of these biological processes. In addition, L-homoserine induced a strong upregulation of genes in the sulfate reductive assimilation pathway, including those encoding its transport. How this non-canonical amino acid triggers these transcriptomic changes is discussed.
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Affiliation(s)
- Ceren Alkim
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France,Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Daniele Farias
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Julie Fredonnet
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | | | - Pauline Herviou
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Marc Picot
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Nawel Slama
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | | | - Nicolas Morin
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Brice Enjalbert
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean M. François
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France,Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France,*Correspondence: Jean M. François,
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14
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Cohen Y, Hershberg R. Rapid Adaptation Often Occurs through Mutations to the Most Highly Conserved Positions of the RNA Polymerase Core Enzyme. Genome Biol Evol 2022; 14:evac105. [PMID: 35876137 PMCID: PMC9459352 DOI: 10.1093/gbe/evac105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations to the genes encoding the RNA polymerase core enzyme (RNAPC) and additional housekeeping regulatory genes were found to be involved in adaptation, in the context of numerous evolutionary experiments, in which bacteria were exposed to diverse selective pressures. This provides a conundrum, as the housekeeping genes that were so often mutated in response to these diverse selective pressures tend to be among the genes that are most conserved in their sequences across the bacterial phylogeny. In order to further examine this apparent discrepancy, we characterized the precise positions of the RNAPC involved in adaptation to a large variety of selective pressures. We found that RNAPC lab adaptations tended to occur at positions displaying traits associated with higher selective constraint. Specifically, compared to other RNAPC positions, positions involved in adaptation tended to be more conserved in their sequences within bacteria, were more often located within defined protein domains, and were located closer to the complex's active site. Higher sequence conservation was also found for resource exhaustion adaptations occurring within additional housekeeping genes. Combined, our results demonstrate that the positions that change most readily in response to well-defined selective pressures exerted in lab environments are often also those that evolve most slowly in nature.
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Affiliation(s)
- Yasmin Cohen
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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15
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Smith TM, Youngblom MA, Kernien JF, Mohamed MA, Fry SS, Bohr LL, Mortimer TD, O'Neill MB, Pepperell CS. Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. eLife 2022; 11:e78454. [PMID: 35726854 PMCID: PMC9213004 DOI: 10.7554/elife.78454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/15/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.
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Affiliation(s)
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - John F Kernien
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Mohamed A Mohamed
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Sydney S Fry
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Mary B O'Neill
- Laboratoire de Biochimie (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL UniversitéParisFrance
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
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16
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Liu YN, Chen RM, Pu QT, Nneji LM, Sun YB. Expression Plasticity of Transposable Elements is Highly Associated with Organismal Re-adaptation to Ancestral Environments. Genome Biol Evol 2022; 14:6596371. [PMID: 35642321 PMCID: PMC9174648 DOI: 10.1093/gbe/evac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Understanding the roles of phenotypic plasticity in adaptive evolution has gained recognition for decades. Studies involving multiple taxa have shown that gene expression plasticity serves as “long-term memory” to facilitate re-adaptations to ancestral environments. Nevertheless, the general pattern and the underlying genetic basis of expression plasticity remain unclear. The transposable elements (TEs) play crucial roles in gene expression regulation and are widely distributed within the genome. Given this, we re-analyzed the transcriptomic data of chicken (Gallus gallus) generated from a reciprocal transplant experiment to examine whether expression shifts of TEs are involved in the re-adaptation process. Similar to the protein-coding genes, the plastic changes of TEs overwhelmingly exceed the genetic changes in the re-adaptation process. Further, the associated TEs co-expressed with diverse genes to perform a regulatory activity. Thus, our study supports the general function of phenotypic plasticity in adaptive evolution, and suggests a regulatory functions of TEs in this process.
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Affiliation(s)
- Yan-Nan Liu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China
| | - Rong-Mei Chen
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China
| | - Qi-Ting Pu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, NJ, 08544, USA
| | - Yan-Bo Sun
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China.,Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
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17
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Pal A, Iyer MS, Srinivasan S, Narain Seshasayee AS, Venkatesh KV. Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology. Open Biol 2022; 12:210206. [PMID: 35167766 PMCID: PMC8846999 DOI: 10.1098/rsob.210206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Evolution facilitates emergence of fitter phenotypes by efficient allocation of cellular resources in conjunction with beneficial mutations. However, system-wide pleiotropic effects that redress the perturbations to the apex node of the transcriptional regulatory networks remain unclear. Here, we elucidate that absence of global transcriptional regulator CRP in Escherichia coli results in alterations in key metabolic pathways under glucose respiratory conditions, favouring stress- or hedging-related functions over growth-enhancing functions. Further, we disentangle the growth-mediated effects from the CRP regulation-specific effects on these metabolic pathways. We quantitatively illustrate that the loss of CRP perturbs proteome efficiency, as evident from metabolic as well as ribosomal proteome fractions, that corroborated with intracellular metabolite profiles. To address how E. coli copes with such systemic defect, we evolved Δcrp mutant in the presence of glucose. Besides acquiring mutations in the promoter of glucose transporter ptsG, the evolved populations recovered the metabolic pathways to their pre-perturbed state coupled with metabolite re-adjustments, which altogether enabled increased growth. By contrast to Δcrp mutant, the evolved strains remodelled their proteome efficiency towards biomass synthesis, albeit at the expense of carbon efficiency. Overall, we comprehensively illustrate the genetic and metabolic basis of pleiotropic effects, fundamental for understanding the growth physiology.
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Affiliation(s)
- Ankita Pal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mahesh S. Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sumana Srinivasan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - K. V. Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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18
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Environmental dependence of competitive fitness in rifampin-resistant
rpoB
mutants of
Bacillus subtilis. Appl Environ Microbiol 2022; 88:e0242221. [DOI: 10.1128/aem.02422-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase (RNAP) is a highly conserved macromolecular machine that contributes to the flow of genetic information from genotype to phenotype. In
Bacillus subtilis
, mutations in the
rpoB
gene encoding the β-subunit of RNAP have been shown to alter a number of global phenotypes including growth, utilization of unusual nutrient sources, sporulation, germination, and production of secondary metabolites. In addition, the spectrum of mutations in
rpoB
leading to rifampin resistance (Rif
R
) can change dramatically depending upon the environment to which
B. subtilis
cells or spores are exposed. Rif
R
rpoB
mutations have historically been associated with slower growth and reduced fitness; however, these assessments of fitness were conducted on limited collections of mutants in rich laboratory media that poorly reflect natural environments typically inhabited by
B. subtilis
. Using a novel, deep-sequencing approach in addition to traditional measurements of growth rate, lag time, and pairwise competitions, we demonstrated the competitive advantage of specific
rpoB
alleles differs depending on the growth environment in which they are determined.
IMPORTANCE
Microbial resistance to antibiotics is a growing threat to public health across the world. Historically, resistance to antibiotics has been associated with reduced fitness. A growing body of evidence indicates that resistance to rifampin, a frontline antibiotic used to treat mycobacterial and biofilm-associated infections, may increase fitness given an appropriate environment even in the absence of the selective antibiotic. Here we experimentally confirm this phenomenon by directly comparing the fitness of multiple rifampin-resistant mutants of
Bacillus subtilis
in rich LB medium and an asparagine minimal medium. Our research demonstrates that the fitness cost of rifampin resistance can vary greatly depending upon the environment. This has important implications for understanding how microbes develop antimicrobial resistance in the absence of antibiotic selection.
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19
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Maire J, van Oppen MJH. A role for bacterial experimental evolution in coral bleaching mitigation? Trends Microbiol 2021; 30:217-228. [PMID: 34429226 DOI: 10.1016/j.tim.2021.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
Coral reefs are rapidly declining because of widespread mass coral bleaching causing extensive coral mortality. Elevated seawater temperatures are the main drivers of coral bleaching, and climate change is increasing the frequency and severity of destructive marine heatwaves. Efforts to enhance coral thermal bleaching tolerance can be targeted at the coral host or at coral-associated microorganisms (e.g., dinoflagellate endosymbionts and bacteria). The literature on experimental evolution of bacteria suggests that it has value as a tool to increase coral climate resilience. We provide a workflow on how to experimentally evolve coral-associated bacteria to confer thermal tolerance to coral hosts and emphasize the value of implementing this approach in coral reef conservation and restoration efforts.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia.
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia; Australian Institute of Marine Science, Townsville, QLD, Australia
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20
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Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance. Antimicrob Agents Chemother 2021; 65:e0050421. [PMID: 34228548 PMCID: PMC8370218 DOI: 10.1128/aac.00504-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a threat to global health and the economy. Rifampicin-resistant Mycobacterium tuberculosis accounts for a third of the global AMR burden. Gaining the upper hand on AMR requires a deeper understanding of the physiology of resistance. AMR often results in a fitness cost in the absence of drug. Identifying the molecular mechanisms underpinning this cost could help strengthen future treatment regimens. Here, we used a collection of M. tuberculosis strains that provide an evolutionary and phylogenetic snapshot of rifampicin resistance and subjected them to genome-wide transcriptomic and proteomic profiling to identify key perturbations of normal physiology. We found that the clinically most common rifampicin resistance-conferring mutation, RpoB Ser450Leu, imparts considerable gene expression changes, many of which are mitigated by the compensatory mutation in RpoC Leu516Pro. However, our data also provide evidence for pervasive epistasis—the same resistance mutation imposed a different fitness cost and functionally distinct changes to gene expression in genetically unrelated clinical strains. Finally, we report a likely posttranscriptional modulation of gene expression that is shared in most of the tested strains carrying RpoB Ser450Leu, resulting in an increased abundance of proteins involved in central carbon metabolism. These changes contribute to a more general trend in which the disruption of the composition of the proteome correlates with the fitness cost of the RpoB Ser450Leu mutation in different strains.
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21
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Pepi M, Focardi S. Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5723. [PMID: 34073520 PMCID: PMC8198758 DOI: 10.3390/ijerph18115723] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/11/2021] [Accepted: 05/22/2021] [Indexed: 12/30/2022]
Abstract
Aquaculture is the productive activity that will play a crucial role in the challenges of the millennium, such as the need for proteins that support humans and the respect for the environment. Aquaculture is an important economic activity in the Mediterranean basin. A great impact is presented, however, by aquaculture practices as they involve the use of antibiotics for treatment and prophylaxis. As a consequence of the use of antibiotics in aquaculture, antibiotic resistance is induced in the surrounding bacteria in the column water, sediment, and fish-associated bacterial strains. Through horizontal gene transfer, bacteria can diffuse antibiotic-resistance genes and mobile resistance genes further spreading genetic determinants. Once triggered, antibiotic resistance easily spreads among aquatic microbial communities and, from there, can reach human pathogenic bacteria, making vain the use of antibiotics for human health. Climate change claims a significant role in this context, as rising temperatures can affect cell physiology in bacteria in the same way as antibiotics, causing antibiotic resistance to begin with. The Mediterranean Sea represents a 'hot spot' in terms of climate change and aspects of antibiotic resistance in aquaculture in this area can be significantly amplified, thus increasing threats to human health. Practices must be adopted to counteract negative impacts on human health, with a reduction in the use of antibiotics as a pivotal point. In the meantime, it is necessary to act against climate change by reducing anthropogenic impacts, for example by reducing CO2 emissions into the atmosphere. The One Health type approach, which involves the intervention of different skills, such as veterinary, ecology, and medicine in compliance with the principles of sustainability, is necessary and strongly recommended to face these important challenges for human and animal health, and for environmental safety in the Mediterranean area.
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Affiliation(s)
- Milva Pepi
- Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Silvano Focardi
- Department of Environmental Sciences, Università di Siena, Via Mattioli, 4, 53100 Siena, Italy
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22
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Hall JPJ, Wright RCT, Guymer D, Harrison E, Brockhurst MA. Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways. MICROBIOLOGY-SGM 2020; 166:56-62. [PMID: 31613206 DOI: 10.1099/mic.0.000862] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The acquisition of plasmids is often accompanied by fitness costs such that compensatory evolution is required to allow plasmid survival, but it is unclear whether compensatory evolution can be extensive or rapid enough to maintain plasmids when they are very costly. The mercury-resistance plasmid pQBR55 drastically reduced the growth of its host, Pseudomonas fluorescens SBW25, immediately after acquisition, causing a small colony phenotype. However, within 48 h of growth on agar plates we observed restoration of the ancestral large colony morphology, suggesting that compensatory mutations had occurred. Relative fitness of these evolved strains, in lab media and in soil microcosms, varied between replicates, indicating different mutational mechanisms. Using genome sequencing we identified that restoration was associated with chromosomal mutations in either a hypothetical DNA-binding protein PFLU4242, RNA polymerase or the GacA/S two-component system. Targeted deletions in PFLU4242, gacA or gacS recapitulated the ameliorated phenotype upon plasmid acquisition, indicating three distinct mutational pathways to compensation. Our data shows that plasmid compensatory evolution is fast enough to allow survival of a plasmid despite it imposing very high fitness costs upon its host, and indeed may regularly occur during the process of isolating and selecting individual plasmid-containing clones.
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Affiliation(s)
- James P J Hall
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.,Department of Evolution, Ecology and Behaviour, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Rosanna C T Wright
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - David Guymer
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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23
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Batarseh TN, Hug SM, Batarseh SN, Gaut BS. Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli. Genome Biol Evol 2020; 12:2029-2044. [PMID: 32785667 PMCID: PMC7750951 DOI: 10.1093/gbe/evaa174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 11/30/2022] Open
Abstract
Evolutionary rescue occurs when adaptation restores population growth against a lethal stressor. Here, we studied evolutionary rescue by conducting experiments with Escherichia coli at the lethal temperature of 43.0 °C, to determine the adaptive mutations that drive rescue and to investigate their effects on fitness and gene expression. From hundreds of populations, we observed that ∼9% were rescued by genetic adaptations. We sequenced 26 populations and identified 29 distinct mutations. Of these populations, 21 had a mutation in the hslVU or rpoBC operon, suggesting that mutations in either operon could drive rescue. We isolated seven strains of E. coli carrying a putative rescue mutation in either the hslVU or rpoBC operon to investigate the mutations’ effects. The single rescue mutations increased E. coli’s relative fitness by an average of 24% at 42.2 °C, but they decreased fitness by 3% at 37.0 °C, illustrating that antagonistic pleiotropy likely affected the establishment of rescue in our system. Gene expression analysis revealed only 40 genes were upregulated across all seven mutations, and these were enriched for functions in translational and flagellar production. As with previous experiments with high temperature adaptation, the rescue mutations tended to restore gene expression toward the unstressed state, but they also caused a higher proportion of novel gene expression patterns. Overall, we find that rescue is infrequent, that it is facilitated by a limited number of mutational targets, and that rescue mutations may have qualitatively different effects than mutations that arise from evolution to nonlethal stressors.
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Affiliation(s)
| | - Shaun M Hug
- Department of Ecology and Evolutionary Biology, UC Irvine
| | | | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine
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24
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Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival. mSystems 2020; 5:5/4/e00364-20. [PMID: 32753505 PMCID: PMC7406224 DOI: 10.1128/msystems.00364-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we began to unravel the cells' responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold shock. By competing cells lacking these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment and lead to identification of novel functions of proteins.IMPORTANCE Experimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses that cells experience in these complex environments can be challenging. One way to approach this is by determining how cells biochemically acclimate to heterogenous environments. In this study, we began to characterize physiological changes by analyzing the transcriptome of cells in a dynamic complex environment. By characterizing the transcriptional profile of cells in long-term stationary phase, a heterogenous and stressful environment, we can begin to understand how cells physiologically and biochemically react to the laboratory environment, and how this compares to more-natural conditions.
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25
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Zhang T, Shi XC, Ding R, Xu K, Tremblay PL. The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate. ISME JOURNAL 2020; 14:2078-2089. [PMID: 32398660 DOI: 10.1038/s41396-020-0673-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 02/01/2023]
Abstract
Multiple Fe(III)-reducing Geobacter species including the model Geobacter sulfurreducens are thought to be incapable of carbon dioxide fixation. The discovery of the reversed oxidative tricarboxylic acid cycle (roTCA) for CO2 reduction with citrate synthase as key enzyme raises the possibility that G. sulfurreducens harbors the metabolic potential for chemolithoautotrophic growth. We investigate this hypothesis by transferring G. sulfurreducens PCA serially with Fe(III) as electron acceptor and formate as electron donor and carbon source. The evolved strain T17-3 grew chemolithoautotrophically with a 2.7-fold population increase over 48 h and a Fe(III) reduction rate of 417.5 μM h-1. T17-3 also grew with CO2 as carbon source. Mutations in T17-3 and enzymatic assays point to an adaptation process where the succinyl-CoA synthetase, which is inactive in the wild-type, became active to complete the roTCA cycle. Deletion of the genes coding for the succinyl-CoA synthetase in T17-3 prevented growth with formate as substrate. Enzymatic assays also showed that the citrate synthase can perform the necessary cleavage of citrate for the functional roTCA cycle. These results demonstrate that G. sulfurreducens after adaptation reduced CO2 via the roTCA cycle. This previously hidden metabolism can be harnessed for biotechnological applications and suggests hidden ecological functions for Geobacter.
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Affiliation(s)
- Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China. .,School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, PR China. .,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China.
| | - Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China.,School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, PR China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Ran Ding
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Kai Xu
- Center for Material Research and Analysis, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China. .,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China.
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26
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Ho WC, Li D, Zhu Q, Zhang J. Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments. SCIENCE ADVANCES 2020; 6:eaba3388. [PMID: 32494748 PMCID: PMC7244318 DOI: 10.1126/sciadv.aba3388] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/12/2020] [Indexed: 05/30/2023]
Abstract
Phenotypic plasticity refers to environment-induced phenotypic changes without mutation and is present in all organisms. The role of phenotypic plasticity in organismal adaptations to novel environments has attracted much attention, but its role in readaptations to ancestral environments is understudied. To address this question, we use the reciprocal transplant approach to investigate the multitissue transcriptomes of chickens adapted to the Tibetan Plateau and adjacent lowland. While many genetic transcriptomic changes had occurred in the forward adaptation to the highland, plastic changes largely transform the transcriptomes to the preferred state when Tibetan chickens are brought back to the lowland. The same trend holds for egg hatchability, a key component of the chicken fitness. These findings, along with highly similar patterns in comparable experiments of guppies and Escherichia coli, demonstrate that organisms generally "remember" their ancestral environments via phenotypic plasticity and reveal a mechanism by which past experience affects future evolution.
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Affiliation(s)
- Wei-Chin Ho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Rodríguez-Verdugo A, Lozano-Huntelman N, Cruz-Loya M, Savage V, Yeh P. Compounding Effects of Climate Warming and Antibiotic Resistance. iScience 2020; 23:101024. [PMID: 32299057 PMCID: PMC7160571 DOI: 10.1016/j.isci.2020.101024] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria have evolved diverse mechanisms to survive environments with antibiotics. Temperature is both a key factor that affects the survival of bacteria in the presence of antibiotics and an environmental trait that is drastically increasing due to climate change. Therefore, it is timely and important to understand links between temperature changes and selection of antibiotic resistance. This review examines these links by synthesizing results from laboratories, hospitals, and environmental studies. First, we describe the transient physiological responses to temperature that alter cellular behavior and lead to antibiotic tolerance and persistence. Second, we focus on the link between thermal stress and the evolution and maintenance of antibiotic resistance mutations. Finally, we explore how local and global changes in temperature are associated with increases in antibiotic resistance and its spread. We suggest that a multidisciplinary, multiscale approach is critical to fully understand how temperature changes are contributing to the antibiotic crisis.
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Affiliation(s)
| | - Natalie Lozano-Huntelman
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mauricio Cruz-Loya
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Van Savage
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pamela Yeh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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28
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Doin de Moura GG, Remigi P, Masson-Boivin C, Capela D. Experimental Evolution of Legume Symbionts: What Have We Learnt? Genes (Basel) 2020; 11:E339. [PMID: 32210028 PMCID: PMC7141107 DOI: 10.3390/genes11030339] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/17/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L.. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica-C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.
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Affiliation(s)
| | | | | | - Delphine Capela
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31320, France; (G.G.D.d.M.); (P.R.); (C.M.-B.)
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29
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Choudhury D, Saini S. Evolution of Escherichia coli in different carbon environments for 2,000 generations. J Evol Biol 2019; 32:1331-1341. [PMID: 31397932 DOI: 10.1111/jeb.13517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/30/2019] [Accepted: 07/29/2019] [Indexed: 11/28/2022]
Abstract
Cellular energetics is thought to have played a key role in dictating all major evolutionary transitions in the history of life on Earth. However, how exactly cellular energetics and metabolism come together to shape evolutionary paths is not well understood. In particular, when an organism is evolved in different energy environments, what are the phenomenological differences in the chosen evolutionary trajectories, is a question that is not well understood. In this context, starting from an Escherichia coli K-12 strain, we evolve the bacterium in five different carbon environments-glucose, arabinose, xylose, rhamnose and a mixture of these four sugars (in a predefined ratio) for approximately 2,000 generations. At the end of the adaptation period, we quantify and compare the growth dynamics of the strains in a variety of environments. The evolved strains show no specialized adaptation towards growth in the carbon medium in which they were evolved. Rather, in all environments, the evolved strains exhibited a reduced lag phase and an increased growth rate. Sequencing results reveal that these dynamical properties are not introduced via mutations in the precise loci associated with utilization of the sugar in which the bacterium evolved. These phenotypic changes are rather likely introduced via mutations elsewhere on the genome. Data from our experiments indicate that evolution in a defined environment does not alter hierarchy in mixed-sugar utilization in bacteria.
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Affiliation(s)
- Debika Choudhury
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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30
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Zhang T, Shi XC, Xia Y, Mai L, Tremblay PL. Escherichia coli adaptation and response to exposure to heavy atmospheric pollution. Sci Rep 2019; 9:10879. [PMID: 31350435 PMCID: PMC6659633 DOI: 10.1038/s41598-019-47427-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
90% of the world population is exposed to heavy atmospheric pollution. This is a major public health issue causing 7 million death each year. Air pollution comprises an array of pollutants such as particulate matters, ozone and carbon monoxide imposing a multifactorial stress on living cells. Here, Escherichia coli was used as model cell and adapted for 390 generations to atmospheric pollution to assess its long-term effects at the genetic, transcriptomic and physiological levels. Over this period, E. coli evolved to grow faster and acquired an adaptive mutation in rpoB, which encodes the RNA polymerase β subunit. Transcriptomic and biochemical characterization showed alteration of the cell membrane composition resulting in lesser permeability after the adaptation process. A second significant change in the cell wall structure of the adapted strain was the greater accumulation of the exopolysaccharides colanic acid and cellulose in the extracellular fraction. Results also indicated that amino acids homeostasis was involved in E. coli response to atmospheric pollutants. This study demonstrates that adaptive mutation with transformative physiological impact can be fixed in genome after exposure to atmospheric pollution and also provides a comprehensive portrait of the cellular response mechanisms involved.
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Affiliation(s)
- Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, P.R. China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, P.R. China
| | - Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, P.R. China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, P.R. China
| | - Yangyang Xia
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, P.R. China
| | - Liqiang Mai
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, P.R. China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, P.R. China. .,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, P.R. China.
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31
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Remigi P, Masson-Boivin C, Rocha EP. Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions. Trends Microbiol 2019; 27:623-634. [DOI: 10.1016/j.tim.2019.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
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32
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Ho WC, Zhang J. Genetic Gene Expression Changes during Environmental Adaptations Tend to Reverse Plastic Changes Even after the Correction for Statistical Nonindependence. Mol Biol Evol 2019; 36:604-612. [PMID: 30649427 DOI: 10.1093/molbev/msz002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organismal adaptations to new environments often begin with plastic phenotypic changes followed by genetic phenotypic changes, but the relationship between the two types of changes is controversial. Contrary to the view that plastic changes serve as steppingstones to genetic adaptations, recent transcriptome studies reported that genetic gene expression changes more often reverse than reinforce plastic expression changes in experimental evolution. However, it was pointed out that this trend could be an artifact of the statistical nonindependence between the estimates of plastic and genetic phenotypic changes, because both estimates rely on the phenotypic measure at the plastic stage. Using computer simulation, we show that indeed the nonindependence can cause an apparent excess of expression reversion relative to reinforcement. We propose a parametric bootstrap method and show by simulation that it removes the bias almost entirely. Analyzing transcriptome data from a total of 34 parallel lines in 5 experimental evolution studies of Escherichia coli, yeast, and guppies that are amenable to our method confirms that genetic expression changes tend to reverse plastic changes. Thus, at least for gene expression traits, phenotypic plasticity does not generally facilitate genetic adaptation. Several other comparisons of statistically nonindependent estimates are commonly performed in evolutionary genomics such as that between cis- and trans-effects of mutations on gene expression and that between transcriptional and translational effects on gene expression. It is important to validate previous results from such comparisons, and our proposed statistical analyses can be useful for this purpose.
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Affiliation(s)
- Wei-Chin Ho
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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33
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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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34
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Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau. Sci Rep 2018; 8:11640. [PMID: 30076357 PMCID: PMC6076244 DOI: 10.1038/s41598-018-30147-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/24/2018] [Indexed: 11/15/2022] Open
Abstract
Deceptive pollination is key to the species richness of Orchidaceae. However, the genetic basis of species diversification is still under study. Section Trigonopedia is a monophyletic clade of genus Cypripedium distributed in the southwest of China. The species of this section are pollinated by different flies. Pollinator differentiation makes section Trigonopedia an ideal group for studying the genetic basis underlying species diversification. Here, we sequenced the transcriptomes of eight species of the genus Cypripedium, including six co-flowering species of section Trigonopedia and two species outside this section as an outgroup. We reconstructed the phylogeny of the section with the combined 1572 single-copy genes extracted from the eight species and produced a highly resolved tree of the section. Furthermore, we combined substitution rate estimation and differential expression analysis to identify candidate genes, including genes related to floral scent synthesis and environmental adaptation, involved in species differentiation. Field investigations showed that these species have adapted to different habitats. We propose that the species diversification in this section is initiated by floral scent differentiation, followed by habitat differentiation, finally leading to speciation. This study sheds novel light on the diversification of closely related orchid species in the Qinghai-Tibetan region.
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35
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Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. eLife 2018; 7:e31867. [PMID: 29620524 PMCID: PMC5919758 DOI: 10.7554/elife.31867] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Cells adapt to familiar changes in their environment by activating predefined regulatory programs that establish adaptive gene expression states. These hard-wired pathways, however, may be inadequate for adaptation to environments never encountered before. Here, we reveal evidence for an alternative mode of gene regulation that enables adaptation to adverse conditions without relying on external sensory information or genetically predetermined cis-regulation. Instead, individual genes achieve optimal expression levels through a stochastic search for improved fitness. By focusing on improving the overall health of the cell, the proposed stochastic tuning mechanism discovers global gene expression states that are fundamentally new and yet optimized for novel environments. We provide experimental evidence for stochastic tuning in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery.
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Affiliation(s)
- Peter L Freddolino
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Jamie Yang
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Amir Momen-Roknabadi
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Saeed Tavazoie
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
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36
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Ibacache-Quiroga C, Oliveros JC, Couce A, Blázquez J. Parallel Evolution of High-Level Aminoglycoside Resistance in Escherichia coli Under Low and High Mutation Supply Rates. Front Microbiol 2018; 9:427. [PMID: 29615988 PMCID: PMC5867336 DOI: 10.3389/fmicb.2018.00427] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/22/2018] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance is a major concern in public health worldwide, thus there is much interest in characterizing the mutational pathways through which susceptible bacteria evolve resistance. Here we use experimental evolution to explore the mutational pathways toward aminoglycoside resistance, using gentamicin as a model, under low and high mutation supply rates. Our results show that both normo and hypermutable strains of Escherichia coli are able to develop resistance to drug dosages > 1,000-fold higher than the minimal inhibitory concentration for their ancestors. Interestingly, such level of resistance was often associated with changes in susceptibility to other antibiotics, most prominently with increased resistance to fosfomycin. Whole-genome sequencing revealed that all resistant derivatives presented diverse mutations in five common genetic elements: fhuA, fusA and the atpIBEFHAGDC, cyoABCDE, and potABCD operons. Despite the large number of mutations acquired, hypermutable strains did not pay, apparently, fitness cost. In contrast to recent studies, we found that the mutation supply rate mainly affected the speed (tempo) but not the pattern (mode) of evolution: both backgrounds acquired the mutations in the same order, although the hypermutator strain did it faster. This observation is compatible with the adaptive landscape for high-level gentamicin resistance being relatively smooth, with few local maxima; which might be a common feature among antibiotics for which resistance involves multiple loci.
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Affiliation(s)
- Claudia Ibacache-Quiroga
- Centro Nacional de Biotecnología, Madrid, Spain.,Centro de Micro-Bioinnovación, Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | | | - Alejandro Couce
- Unité Mixte de Recherche 1137, Infection, Antimicrobiens, Modélisation, Evolution, INSERM, Université Paris Diderot, Paris, France
| | - Jesus Blázquez
- Centro Nacional de Biotecnología, Madrid, Spain.,Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, Sevilla, Spain
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37
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Ho WC, Zhang J. Evolutionary adaptations to new environments generally reverse plastic phenotypic changes. Nat Commun 2018; 9:350. [PMID: 29367589 PMCID: PMC5783951 DOI: 10.1038/s41467-017-02724-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/20/2017] [Indexed: 11/25/2022] Open
Abstract
Organismal adaptation to a new environment may start with plastic phenotypic changes followed by genetic changes, but whether the plastic changes are stepping stones to genetic adaptation is debated. Here we address this question by investigating gene expression and metabolic flux changes in the two-phase adaptation process using transcriptomic data from multiple experimental evolution studies and computational metabolic network analysis, respectively. We discover that genetic changes more frequently reverse than reinforce plastic phenotypic changes in virtually every adaptation. Metabolic network analysis reveals that, even in the presence of plasticity, organismal fitness drops after environmental shifts, but largely recovers through subsequent evolution. Such fitness trajectories explain why plastic phenotypic changes are genetically compensated rather than strengthened. In conclusion, although phenotypic plasticity may serve as an emergency response to a new environment that is necessary for survival, it does not generally facilitate genetic adaptation by bringing the organismal phenotype closer to the new optimum. Phenotypic plasticity has been suggested to facilitate survival in new environments and subsequent adaptation. Here, the authors reanalyze transcriptomic data from experimental evolution studies in combination with computational metabolic network analysis and show that genetic adaptation tends to reverse plastic changes in order to recover fitness.
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Affiliation(s)
- Wei-Chin Ho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.,Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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38
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Linzner KA, Kent AG, Martiny AC. Evolutionary Pathway Determines the Stoichiometric Response of Escherichia coli Adapted to High Temperature. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2017.00173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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39
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Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments. Genetics 2017; 208:307-322. [PMID: 29141909 DOI: 10.1534/genetics.117.300519] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 10/21/2017] [Indexed: 11/18/2022] Open
Abstract
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change.
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40
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Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. mBio 2017; 8:mBio.01780-17. [PMID: 29138306 PMCID: PMC5686539 DOI: 10.1128/mbio.01780-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection.IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.
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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.
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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
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Graves JL, Thomas M, Ewunkem JA. Antimicrobial Nanomaterials: Why Evolution Matters. NANOMATERIALS 2017; 7:nano7100283. [PMID: 28934114 PMCID: PMC5666448 DOI: 10.3390/nano7100283] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 01/25/2023]
Abstract
Due to the widespread occurrence of multidrug resistant microbes there is increasing interest in the use of novel nanostructured materials as antimicrobials. Specifically, metallic nanoparticles such as silver, copper, and gold have been deployed due to the multiple impacts they have on bacterial physiology. From this, many have concluded that such nanomaterials represent steep obstacles against the evolution of resistance. However, we have already shown that this view is fallacious. For this reason, the significance of our initial experiments are beginning to be recognized in the antimicrobial effects of nanomaterials literature. This recognition is not yet fully understood and here we further explain why nanomaterials research requires a more nuanced understanding of core microbial evolution principles.
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Affiliation(s)
- Joseph L Graves
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC 27401, USA.
| | - Misty Thomas
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA.
| | - Jude Akamu Ewunkem
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC 27401, USA.
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Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures. Proc Natl Acad Sci U S A 2017; 114:E1904-E1912. [PMID: 28202733 DOI: 10.1073/pnas.1616132114] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations of Escherichia coli were evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily alternations between 32 °C and 42 °C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated ∼5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited ∼17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only ∼4%. For example, all six strains evolved at 32 °C had mutations in nadR, whereas none of the other 24 strains did. However, a population evolved at 37 °C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when tested in the others, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments.
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Claessens A, Affara M, Assefa SA, Kwiatkowski DP, Conway DJ. Culture adaptation of malaria parasites selects for convergent loss-of-function mutants. Sci Rep 2017; 7:41303. [PMID: 28117431 PMCID: PMC5259787 DOI: 10.1038/srep41303] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022] Open
Abstract
Cultured human pathogens may differ significantly from source populations. To investigate the genetic basis of laboratory adaptation in malaria parasites, clinical Plasmodium falciparum isolates were sampled from patients and cultured in vitro for up to three months. Genome sequence analysis was performed on multiple culture time point samples from six monoclonal isolates, and single nucleotide polymorphism (SNP) variants emerging over time were detected. Out of a total of five positively selected SNPs, four represented nonsense mutations resulting in stop codons, three of these in a single ApiAP2 transcription factor gene, and one in SRPK1. To survey further for nonsense mutants associated with culture, genome sequences of eleven long-term laboratory-adapted parasite strains were examined, revealing four independently acquired nonsense mutations in two other ApiAP2 genes, and five in Epac. No mutants of these genes exist in a large database of parasite sequences from uncultured clinical samples. This implicates putative master regulator genes in which multiple independent stop codon mutations have convergently led to culture adaptation, affecting most laboratory lines of P. falciparum. Understanding the adaptive processes should guide development of experimental models, which could include targeted gene disruption to adapt fastidious malaria parasite species to culture.
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Affiliation(s)
- Antoine Claessens
- London School of Hygiene and Tropical Medicine, London, UK
- Medical Research Council Unit The Gambia, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Muna Affara
- Medical Research Council Unit The Gambia, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
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Digianantonio KM, Hecht MH. A protein constructed de novo enables cell growth by altering gene regulation. Proc Natl Acad Sci U S A 2016; 113:2400-5. [PMID: 26884172 PMCID: PMC4780649 DOI: 10.1073/pnas.1600566113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent advances in protein design rely on rational and computational approaches to create novel sequences that fold and function. In contrast, natural systems selected functional proteins without any design a priori. In an attempt to mimic nature, we used large libraries of novel sequences and selected for functional proteins that rescue Escherichia coli cells in which a conditionally essential gene has been deleted. In this way, the de novo protein SynSerB3 was selected as a rescuer of cells in which serB, which encodes phosphoserine phosphatase, an enzyme essential for serine biosynthesis, was deleted. However, SynSerB3 does not rescue the deleted activity by catalyzing hydrolysis of phosphoserine. Instead, SynSerB3 up-regulates hisB, a gene encoding histidinol phosphate phosphatase. This endogenous E. coli phosphatase has promiscuous activity that, when overexpressed, compensates for the deletion of phosphoserine phosphatase. Thus, the de novo protein SynSerB3 rescues the deletion of serB by altering the natural regulation of the His operon.
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Affiliation(s)
| | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, NJ 08540
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De Maeyer D, Weytjens B, De Raedt L, Marchal K. Network-Based Analysis of eQTL Data to Prioritize Driver Mutations. Genome Biol Evol 2016; 8:481-94. [PMID: 26802430 PMCID: PMC4825419 DOI: 10.1093/gbe/evw010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive phenotype by affecting the same molecular pathways, a phenomenon referred to as parallelism at the molecular pathway level. This implies that successful driver identification depends on interpreting mutated genes in terms of molecular networks. Driver identification and obtaining a network-based understanding of the adaptive phenotype are thus confounded problems that ideally should be solved simultaneously. In this study, a network-based eQTL method is presented that solves both the driver identification and the network-based interpretation problem. As input the method uses coupled genotype-expression phenotype data (eQTL data) of independently evolved lines with similar adaptive phenotypes and an organism-specific genome-wide interaction network. The search for mutational consistency at pathway level is defined as a subnetwork inference problem, which consists of inferring a subnetwork from the genome-wide interaction network that best connects the genes containing mutations to differentially expressed genes. Based on their connectivity with the differentially expressed genes, mutated genes are prioritized as driver genes. Based on semisynthetic data and two publicly available data sets, we illustrate the potential of the network-based eQTL method to prioritize driver genes and to gain insights in the molecular mechanisms underlying an adaptive phenotype. The method is available at http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.html
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Affiliation(s)
- Dries De Maeyer
- Deptartment of Information Technology (INTEC, iMINDS), UGent, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Weytjens
- Deptartment of Information Technology (INTEC, iMINDS), UGent, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Luc De Raedt
- Department of Computer Science, KU Leuven, Celestijnenlaan 200A, B-3001 Leuven, Belgium
| | - Kathleen Marchal
- Deptartment of Information Technology (INTEC, iMINDS), UGent, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium Department of Genetics, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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