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Green R, Wang H, Botchey C, Zhang SNN, Wadsworth C, Tyrrell F, Letton J, McBain AJ, Paszek P, Krašovec R, Knight CG. Collective peroxide detoxification determines microbial mutation rate plasticity in E. coli. PLoS Biol 2024; 22:e3002711. [PMID: 39008532 PMCID: PMC11272383 DOI: 10.1371/journal.pbio.3002711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 07/25/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024] Open
Abstract
Mutagenesis is responsive to many environmental factors. Evolution therefore depends on the environment not only for selection but also in determining the variation available in a population. One such environmental dependency is the inverse relationship between mutation rates and population density in many microbial species. Here, we determine the mechanism responsible for this mutation rate plasticity. Using dynamical computational modelling and in culture mutation rate estimation, we show that the negative relationship between mutation rate and population density arises from the collective ability of microbial populations to control concentrations of hydrogen peroxide. We demonstrate a loss of this density-associated mutation rate plasticity (DAMP) when Escherichia coli populations are deficient in the degradation of hydrogen peroxide. We further show that the reduction in mutation rate in denser populations is restored in peroxide degradation-deficient cells by the presence of wild-type cells in a mixed population. Together, these model-guided experiments provide a mechanistic explanation for DAMP, applicable across all domains of life, and frames mutation rate as a dynamic trait shaped by microbial community composition.
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Affiliation(s)
- Rowan Green
- School of Natural Sciences, Faculty of Science & Engineering, University of Manchester, United Kingdom
| | - Hejie Wang
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Carol Botchey
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Siu Nam Nancy Zhang
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Charles Wadsworth
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Francesca Tyrrell
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - James Letton
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Andrew J. McBain
- School of Health Sciences, Faculty of Biology Medicine & Health, University of Manchester, United Kingdom
| | - Pawel Paszek
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Rok Krašovec
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Christopher G. Knight
- School of Natural Sciences, Faculty of Science & Engineering, University of Manchester, United Kingdom
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2
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Chen M, Wu B, Huang Y, Wang W, Zheng Y, Shabbir S, Liu P, Dai Y, Xia M, Hu G, He M. Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation. Nucleic Acids Res 2024; 52:5643-5657. [PMID: 38716861 PMCID: PMC11162768 DOI: 10.1093/nar/gkae318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 06/11/2024] Open
Abstract
Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome may also play an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutation and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). We find that genomic mutation only influences the local chromosome contacts, whereas stress of acetic acid and furfural restrict the long-range contacts and significantly change the chromosome organization at domain scales. Further deciphering the domain feature unveils the important transcription factors, Ferric uptake regulator (Fur) proteins, which act as nucleoid-associated proteins to promote long-range (>200 kb) chromosomal communications and regulate the expression of genes involved in stress response. Our work suggests that ubiquitous transcription factors in prokaryotes mediate chromosome organization and regulate stress-resistance genes in bacterial adaptation.
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Affiliation(s)
- Mao Chen
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yuhuan Huang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yudi Zheng
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Samina Shabbir
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Panting Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yonghua Dai
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Mengli Xia
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
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3
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Van Eldijk TJB, Sheridan EA, Martin G, Weissing FJ, Kuipers OP, Van Doorn GS. Temperature dependence of the mutation rate towards antibiotic resistance. JAC Antimicrob Resist 2024; 6:dlae085. [PMID: 38847007 PMCID: PMC11154133 DOI: 10.1093/jacamr/dlae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Objectives Environmental conditions can influence mutation rates in bacteria. Fever is a common response to infection that alters the growth conditions of infecting bacteria. Here we examine how a temperature change, such as is associated with fever, affects the mutation rate towards antibiotic resistance. Methods We used a fluctuation test to assess the mutation rate towards antibiotic resistance in Escherichia coli at two different temperatures: 37°C (normal temperature) and 40°C (fever temperature). We performed this measurement for three different antibiotics with different modes of action: ciprofloxacin, rifampicin and ampicillin. Results In all cases, the mutation rate towards antibiotic resistance turned out to be temperature dependent, but in different ways. Fever temperatures led to a reduced mutation rate towards ampicillin resistance and an elevated mutation rate towards ciprofloxacin and rifampicin resistance. Conclusions This study shows that the mutation rate towards antibiotic resistance is impacted by a small change in temperature, such as associated with fever. This opens a new avenue to mitigate the emergence of antibiotic resistance by coordinating the choice of an antibiotic with the decision of whether or not to suppress fever when treating a patient. Hence, optimized combinations of antibiotics and fever suppression strategies may be a new weapon in the battle against antibiotic resistance.
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Affiliation(s)
- Timo J B Van Eldijk
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Eleanor A Sheridan
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Guillaume Martin
- Institut des Sciences de l’Evolution de Montpellier UMR5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - G Sander Van Doorn
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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4
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Johnson MTJ, Arif I, Marchetti F, Munshi-South J, Ness RW, Szulkin M, Verrelli BC, Yauk CL, Anstett DN, Booth W, Caizergues AE, Carlen EJ, Dant A, González J, Lagos CG, Oman M, Phifer-Rixey M, Rennison DJ, Rosenberg MS, Winchell KM. Effects of urban-induced mutations on ecology, evolution and health. Nat Ecol Evol 2024; 8:1074-1086. [PMID: 38641700 DOI: 10.1038/s41559-024-02401-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 04/21/2024]
Abstract
Increasing evidence suggests that urbanization is associated with higher mutation rates, which can affect the health and evolution of organisms that inhabit cities. Elevated pollution levels in urban areas can induce DNA damage, leading to de novo mutations. Studies on mutations induced by urban pollution are most prevalent in humans and microorganisms, whereas studies of non-human eukaryotes are rare, even though increased mutation rates have the potential to affect organisms and their populations in contemporary time. Our Perspective explores how higher mutation rates in urban environments could impact the fitness, ecology and evolution of populations. Most mutations will be neutral or deleterious, and higher mutation rates associated with elevated pollution in urban populations can increase the risk of cancer in humans and potentially other species. We highlight the potential for urban-driven increased deleterious mutational loads in some organisms, which could lead to a decline in population growth of a wide diversity of organisms. Although beneficial mutations are expected to be rare, we argue that higher mutation rates in urban areas could influence adaptive evolution, especially in organisms with short generation times. Finally, we explore avenues for future research to better understand the effects of urban-induced mutations on the fitness, ecology and evolution of city-dwelling organisms.
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Affiliation(s)
- Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada.
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Irtaqa Arif
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, Armonk, NY, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Marta Szulkin
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Warren Booth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, MO, USA
| | - Anthony Dant
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - César González Lagos
- Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Madeleine Oman
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Diana J Rennison
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
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5
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Liu X, Xia X, Liu Y, Li Z, Shi T, Zhang H, Dong Q. Recent advances on the formation, detection, resistance mechanism, and control technology of Listeria monocytogenes biofilm in food industry. Food Res Int 2024; 180:114067. [PMID: 38395584 DOI: 10.1016/j.foodres.2024.114067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
Listeria monocytogenes is an important foodborne pathogen that causes listeriosis, a severe and fatal condition. Biofilms are communities of microorganisms nested within a self-secreted extracellular polymeric substance, and they protect L. monocytogenes from environmental stresses. Biofilms, once formed, can lead to the persistence of L. monocytogenes in processing equipment and are therefore considered to be a major concern for the food industry. This paper briefly introduces the recent advancements on biofilm formation characteristics and detection methods, and focuses on analysis of the mechanism of L. monocytogenes biofilm resistance; Moreover, this paper also summarizes and discusses the existing different techniques of L. monocytogenes biofilm control according to the physical, chemical, biological, and combined strategies, to provide a theoretical reference to aid the choice of effective control technology in the food industry.
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Affiliation(s)
- Xin Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Xuejuan Xia
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Yangtai Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Zhuosi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Tianqi Shi
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China.
| | - Hongzhi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China.
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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6
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Yang T, Zhang S, Pan Y, Li X, Liu G, Sun H, Zhang R, Zhang C. Breeding of high-tolerance yeast by adaptive evolution and high-gravity brewing of mutant. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:686-697. [PMID: 37654243 DOI: 10.1002/jsfa.12959] [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: 03/28/2023] [Revised: 08/13/2023] [Accepted: 09/01/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Ethanol and osmotic stresses are the major limiting factors for brewing strong beer with high-gravity wort. Breeding of yeast strains with high osmotic and ethanol tolerance and studying very-high-gravity (VHG) brewing technology is of great significance for brewing strong beer. RESULTS This study used an optimized microbial microdroplet culture (MMC) system for adaptive laboratory evolution (ALE) of Saccharomyces cerevisiae YN81 to improve its tolerance to osmotic and ethanol stress. Meanwhile, we investigated the VHG and VHG with added ethanol (VHGAE) brewing processes for the evolved mutants in brewing strong beer. The results showed that three evolved mutants were obtained; among them, the growth performance of YN81mc-8.3 under 300, 340, 380, 420 and 460 g L-1 sucrose stresses was greater than that of the other strains. The ethanol tolerance of YN81mc-8.3 was 12%, which was 20% higher than that of YN81. During strong-beer brewing in a 100 L cylindrical cone-bottom tank, the sugar utilization and ethanol yield of YN81mc-8.3 outperformed those of YN81 in both the VHG and VHGAE brewing processes. Measurement of the diacetyl concentration showed that YN81mc-8.3 had a stronger diacetyl reduction ability; in particular, the real degree of fermentation of beers brewed by YN81mc-8.3 in VHG and VHGAE brewing processes was 75.35% and 66.71%, respectively - higher than those of the two samples brewed by YN81. Meanwhile, the visual, olfactive and gustative properties of the strong beer produced by YN81mc-8.3 were better than those of the other beers. CONCLUSION In this study, the mutant YN81mc-8.3 and the VHGAE brewing process were optimal and represented a better alternative strong-beer brewing process. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Tianyou Yang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Shishuang Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an, China
| | - Yuru Pan
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xu Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Gaifeng Liu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Haiyan Sun
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Rongxian Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Chaohui Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
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7
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Horton JS, Taylor TB. Mutation bias and adaptation in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37943288 DOI: 10.1099/mic.0.001404] [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] [Indexed: 11/10/2023]
Abstract
Genetic mutation, which provides the raw material for evolutionary adaptation, is largely a stochastic force. However, there is ample evidence showing that mutations can also exhibit strong biases, with some mutation types and certain genomic positions mutating more often than others. It is becoming increasingly clear that mutational bias can play a role in determining adaptive outcomes in bacteria in both the laboratory and the clinic. As such, understanding the causes and consequences of mutation bias can help microbiologists to anticipate and predict adaptive outcomes. In this review, we provide an overview of the mechanisms and features of the bacterial genome that cause mutational biases to occur. We then describe the environmental triggers that drive these mechanisms to be more potent and outline the adaptive scenarios where mutation bias can synergize with natural selection to define evolutionary outcomes. We conclude by describing how understanding mutagenic genomic features can help microbiologists predict areas sensitive to mutational bias, and finish by outlining future work that will help us achieve more accurate evolutionary forecasts.
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Affiliation(s)
- James S Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
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8
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Lynch M, Ali F, Lin T, Wang Y, Ni J, Long H. The divergence of mutation rates and spectra across the Tree of Life. EMBO Rep 2023; 24:e57561. [PMID: 37615267 PMCID: PMC10561183 DOI: 10.15252/embr.202357561] [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: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Farhan Ali
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
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9
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Garte S. Targeted Hypermutation as a Survival Strategy: A Theoretical Approach. Acta Biotheor 2023; 71:20. [PMID: 37668864 DOI: 10.1007/s10441-023-09471-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.
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Affiliation(s)
- Seymour Garte
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA.
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10
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Cebrián-Sastre E, Chiner-Oms A, Torres-Pérez R, Comas I, Oliveros JC, Blázquez J, Castañeda-García A. Selective Pressure by Rifampicin Modulates Mutation Rates and Evolutionary Trajectories of Mycobacterial Genomes. Microbiol Spectr 2023; 11:e0101723. [PMID: 37436169 PMCID: PMC10433840 DOI: 10.1128/spectrum.01017-23] [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: 03/09/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023] Open
Abstract
Resistance to the frontline antibiotic rifampicin constitutes a challenge to the treatment and control of tuberculosis. Here, we analyzed the mutational landscape of Mycobacterium smegmatis during long-term evolution with increasing concentrations of rifampicin, using a mutation accumulation assay combined with whole-genome sequencing. Antibiotic treatment enhanced the acquisition of mutations, doubling the genome-wide mutation rate of the wild-type cells. While antibiotic exposure led to extinction of almost all wild-type lines, the hypermutable phenotype of the ΔnucS mutant strain (noncanonical mismatch repair deficient) provided an efficient response to the antibiotic, leading to high rates of survival. This adaptative advantage resulted in the emergence of higher levels of rifampicin resistance, an accelerated acquisition of drug resistance mutations in rpoB (β RNA polymerase), and a wider diversity of evolutionary pathways that led to drug resistance. Finally, this approach revealed a subset of adaptive genes under positive selection with rifampicin that could be associated with the development of antibiotic resistance. IMPORTANCE Rifampicin is the most important first-line antibiotic against mycobacterial infections, including tuberculosis, one of the top causes of death worldwide. Acquisition of rifampicin resistance constitutes a major global public health problem that makes the control of the disease challenging. Here, we performed an experimental evolution assay under antibiotic selection to analyze the response and adaptation of mycobacteria, leading to the acquisition of rifampicin resistance. This approach explored the total number of mutations that arose in the mycobacterial genomes under long-term rifampicin exposure, using whole-genome sequencing. Our results revealed the effect of rifampicin at a genomic level, identifying different mechanisms and multiple pathways leading to rifampicin resistance in mycobacteria. Moreover, this study detected that an increase in the rate of mutations led to enhanced levels of drug resistance and survival. In summary, all of these results could be useful to understand and prevent the emergence of drug-resistant isolates in mycobacterial infections.
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Affiliation(s)
- E. Cebrián-Sastre
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - A. Chiner-Oms
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - R. Torres-Pérez
- Servicio de Bioinformática para Genómica y Proteómica. Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - I. Comas
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - J. C. Oliveros
- Servicio de Bioinformática para Genómica y Proteómica. Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - J. Blázquez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - A. Castañeda-García
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (CNM-ISCIII), Majadahonda (Madrid), Spain
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11
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Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics. THE ISME JOURNAL 2023; 17:775-785. [PMID: 36854789 PMCID: PMC10119117 DOI: 10.1038/s41396-023-01381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Predation defense is an important feature of predator-prey interactions adding complexity to ecosystem dynamics. Prey organisms have developed various strategies to escape predation which differ in mode (elude vs. attack), reversibility (inducible vs. permanent), and scope (individual vs. cooperative defenses). While the mechanisms and controls of many singular defenses are well understood, important ecological and evolutionary facets impacting long-term predator-prey dynamics remain underexplored. This pertains especially to trade-offs and interactions between alternative defenses occurring in prey populations evolving under predation pressure. Here, we explored the dynamics of a microbial predator-prey system consisting of bacterivorous flagellates (Poteriospumella lacustris) feeding on Pseudomonas putida. Within five weeks of co-cultivation corresponding to about 35 predator generations, we observed a consistent succession of bacterial defenses in all replicates (n = 16). Initially, bacteria expressed a highly effective cooperative defense based on toxic metabolites, which brought predators close to extinction. This initial strategy, however, was consistently superseded by a second mechanism of predation defense emerging via de novo mutations. Combining experiments with mathematical modeling, we demonstrate how this succession of defenses is driven by the maximization of individual rather than population benefits, highlighting the role of rapid evolution in the breakdown of social cooperation.
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12
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Bhattacharyya S, Bhattacharyya M, Pfannenstiel DM, Nandi AK, Hwang Y, Ho K, Harshey RM. Efflux-linked accelerated evolution of antibiotic resistance at a population edge. Mol Cell 2022; 82:4368-4385.e6. [PMID: 36400010 PMCID: PMC9699456 DOI: 10.1016/j.molcel.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/22/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022]
Abstract
Efflux is a common mechanism of resistance to antibiotics. We show that efflux itself promotes accumulation of antibiotic-resistance mutations (ARMs). This phenomenon was initially discovered in a bacterial swarm where the linked phenotypes of high efflux and high mutation frequencies spatially segregated to the edge, driven there by motility. We have uncovered and validated a global regulatory network connecting high efflux to downregulation of specific DNA-repair pathways even in non-swarming states. The efflux-DNA repair link was corroborated in a clinical "resistome" database: genomes with mutations that increase efflux exhibit a significant increase in ARMs. Accordingly, efflux inhibitors decreased evolvability to antibiotic resistance. Swarms also revealed how bacterial populations serve as a reservoir of ARMs even in the absence of antibiotic selection pressure. High efflux at the edge births mutants that, despite compromised fitness, survive there because of reduced competition. This finding is relevant to biofilms where efflux activity is high.
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Affiliation(s)
- Souvik Bhattacharyya
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX 78712, USA.
| | | | - Dylan M Pfannenstiel
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX 78712, USA
| | - Anjan K Nandi
- Department of Physical Sciences, Indian Institute of Science Education & Research, Kolkata, India
| | - YuneSahng Hwang
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX 78712, USA
| | - Khang Ho
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX 78712, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX 78712, USA.
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13
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Trethowan LA, Arvidsson C, Bramley GLC. Environmental stress influences Malesian Lamiaceae distributions. Ecol Evol 2022; 12:e9467. [PMID: 36340815 PMCID: PMC9627225 DOI: 10.1002/ece3.9467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Dual effects of spatial distance and environment shape archipelagic floras. In Malesia, there are multiple environmental stressors associated with increasing uplands, drought, and metal‐rich ultramafic soils. Here, we examine the contrasting impacts of multifactorial environmental stress and spatial distance upon Lamiaceae species distributions. We used a phylogenetic generalized mixed effects model of species occurrence across Malesia's taxonomic database working group areas from Peninsular Malaysia to New Guinea. Predictor variables were environmental stress, spatial distance between areas and two trait principal component axes responsible for increasing fruit and leaf size and a negative correlation between flower size and plant height. We found that Lamiaceae species with smaller fruits and leaves are more likely to tolerate environmental stress and become widely distributed across megadiverse Malesian islands. How global species distribution and diversification are shaped by multifactorial environmental stress requires further examination.
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Affiliation(s)
| | - Camilla Arvidsson
- Herbarium Kew Royal Botanic Gardens Kew London UK
- Department of Biosciences University of Exeter Exeter UK
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14
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Wang YC, Lu MC, Li YT, Tang HL, Hsiao PY, Chen BH, Teng RH, Chiou CS, Lai YC. Microevolution of CG23-I Hypervirulent Klebsiella pneumoniae during Recurrent Infections in a Single Patient. Microbiol Spectr 2022; 10:e0207722. [PMID: 36129301 PMCID: PMC9602619 DOI: 10.1128/spectrum.02077-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/05/2022] [Indexed: 12/31/2022] Open
Abstract
CG23-I lineage constitutes the majority of hypervirulent Klebsiella pneumoniae. A diabetic patient suffered six episodes of infections caused by CG23-I K. pneumoniae. A total of nine isolates were collected in 2020. We performed whole-genome sequencing to elucidate the within-patient evolution of CG23-I K. pneumoniae. The maximum pairwise difference among the nine longitudinally collected isolates was five single nucleotide polymorphisms. One of the mutations was at the Asp87 position of GyrA. Four indels were identified, including an initiator tRNAfMet duplication, a tRNAArg deletion, a 7-bp insertion, and a 22-bp deletion. All 9 isolates had the genomic features of CG23-I K. pneumoniae, a chromosome-borne ICEKp10, and a large virulence plasmid. The carriage of a complete set of genes for the biosynthesis of colibactin by ICEKp10 gave the nine isolates an ability to cause DNA damage to RAW264.7 cells. Compared with the initial isolate, the last isolate with an additional copy of initiator tRNAfMet grew faster in a nutrient-limiting condition and exhibited enhanced virulence in BALB/c mice. Collectively, we characterized the within-patient microevolution of CG23-I K. pneumoniae through an in-depth comparison of genome sequences. Using the in vitro experiments and mouse models, we also demonstrated that these genomic alterations endowed the isolates with advantages to pass through in vivo selection. IMPORTANCE CG23-I is a significant lineage of hypervirulent Klebsiella pneumoniae. This study characterizes the within-patient microevolution of CG23-I K. pneumoniae. Selective pressures from continuous use of antibiotics favored point mutations contributing to bacterial resistance to antibiotics. The duplication of an initiator tRNAfMet gene helped CG23-I K. pneumoniae proliferate to reach a maximal population size during infections. For longer persistence inside a human host, the large virulence plasmid evolved with more flexible control of replication through duplication of the iteron-1 region. With the genomic alterations, the last isolate had a growth advantage over the initial isolate and exhibited enhanced virulence in BALB/c mice. This study gives us a deeper understanding of the genome evolution during the within-patient pathoadaptation of CG23-I K. pneumoniae.
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Affiliation(s)
- Yao-Chen Wang
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yia-Ting Li
- Division of Respiratory Therapy, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hui-Ling Tang
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Pei-Yi Hsiao
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Bo-Han Chen
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chien-Shun Chiou
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Chyi Lai
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
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15
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Multivariate selection and the making and breaking of mutational pleiotropy. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10195-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractThe role of mutations have been subject to many controversies since the formation of the Modern Synthesis of evolution in the early 1940ties. Geneticists in the early half of the twentieth century tended to view mutations as a limiting factor in evolutionary change. In contrast, natural selection was largely viewed as a “sieve” whose main role was to sort out the unfit but which could not create anything novel alone. This view gradually changed with the development of mathematical population genetics theory, increased appreciation of standing genetic variation and the discovery of more complex forms of selection, including balancing selection. Short-term evolutionary responses to selection are mainly influenced by standing genetic variation, and are predictable to some degree using information about the genetic variance–covariance matrix (G) and the strength and form of selection (e. g. the vector of selection gradients, β). However, predicting long-term evolution is more challenging, and requires information about the nature and supply of novel mutations, summarized by the mutational variance–covariance matrix (M). Recently, there has been increased attention to the role of mutations in general and M in particular. Some evolutionary biologists argue that evolution is largely mutation-driven and claim that mutation bias frequently results in mutation-biased adaptation. Strong similarities between G and M have also raised questions about the non-randomness of mutations. Moreover, novel mutations are typically not isotropic in their phenotypic effects and mutational pleiotropy is common. Here I discuss the evolutionary origin and consequences of mutational pleiotropy and how multivariate selection directly shapes G and indirectly M through changed epistatic relationships. I illustrate these ideas by reviewing recent literature and models about correlational selection, evolution of G and M, sexual selection and the fitness consequences of sexual antagonism.
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16
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Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022; 31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.
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Affiliation(s)
- Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Saacnicteh Toledo‐Patiño
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Lianet Noda‐García
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemRehovotIsrael
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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17
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Kapel N, Caballero JD, MacLean RC. Localized pmrB hypermutation drives the evolution of colistin heteroresistance. Cell Rep 2022; 39:110929. [PMID: 35675785 PMCID: PMC9189680 DOI: 10.1016/j.celrep.2022.110929] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Colistin has emerged as an important last line of defense for the treatment of infections caused by antibiotic-resistant gram-negative pathogens, but colistin resistance remains poorly understood. Here, we investigate the responses of ≈1,000 populations of a multi-drug-resistant (MDR) strain of P. aeruginosa to a high dose of colistin. Colistin exposure causes rapid cell death, but some populations eventually recover due to the growth of sub-populations of heteroresistant cells. Heteroresistance is unstable, and resistance is rapidly lost under culture in colistin-free medium. The evolution of heteroresistance is primarily driven by selection for heteroresistance at two hotspot sites in the PmrAB regulatory system. Localized hypermutation of pmrB generates colistin resistance at 103–104 times the background resistance mutation rate (≈2 × 10-5 per cell division). PmrAB provides resistance to antimicrobial peptides that are involved in host immunity, suggesting that this pathogen may have evolved a highly mutable pmrB as an adaptation to host immunity. Pseudomonas populations recover from colistin due to the growth of heteroresistant cells Heteroresistance is driven by pre-existing mutations in the PmrAB regulatory system pmrB mutations arise at 103–104 times the background mutation rate Heteroresistance is unstable and is rapidly lost in the absence of colistin
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Affiliation(s)
- Natalia Kapel
- University of Oxford, Department of Zoology, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Julio Diaz Caballero
- University of Oxford, Department of Zoology, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - R Craig MacLean
- University of Oxford, Department of Zoology, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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18
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Marti H, Suchland RJ, Rockey DD. The Impact of Lateral Gene Transfer in Chlamydia. Front Cell Infect Microbiol 2022; 12:861899. [PMID: 35321311 PMCID: PMC8936141 DOI: 10.3389/fcimb.2022.861899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Lateral gene transfer (LGT) facilitates many processes in bacterial ecology and pathogenesis, especially regarding pathogen evolution and the spread of antibiotic resistance across species. The obligate intracellular chlamydiae, which cause a range of diseases in humans and animals, were historically thought to be highly deficient in this process. However, research over the past few decades has demonstrated that this was not the case. The first reports of homologous recombination in the Chlamydiaceae family were published in the early 1990s. Later, the advent of whole-genome sequencing uncovered clear evidence for LGT in the evolution of the Chlamydiaceae, although the acquisition of tetracycline resistance in Chlamydia (C.) suis is the only recent instance of interphylum LGT. In contrast, genome and in vitro studies have shown that intraspecies DNA exchange occurs frequently and can even cross species barriers between closely related chlamydiae, such as between C. trachomatis, C. muridarum, and C. suis. Additionally, whole-genome analysis led to the identification of various DNA repair and recombination systems in C. trachomatis, but the exact machinery of DNA uptake and homologous recombination in the chlamydiae has yet to be fully elucidated. Here, we reviewed the current state of knowledge concerning LGT in Chlamydia by focusing on the effect of homologous recombination on the chlamydial genome, the recombination machinery, and its potential as a genetic tool for Chlamydia.
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Affiliation(s)
- Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Hanna Marti,
| | - Robert J. Suchland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
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19
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Mutators Enhance Adaptive Micro-Evolution in Pathogenic Microbes. Microorganisms 2022; 10:microorganisms10020442. [PMID: 35208897 PMCID: PMC8875331 DOI: 10.3390/microorganisms10020442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Adaptation to the changing environmental conditions experienced within a host requires genetic diversity within a microbial population. Genetic diversity arises from mutations which occur due to DNA damage from exposure to exogenous environmental stresses or generated endogenously through respiration or DNA replication errors. As mutations can be deleterious, a delicate balance must be obtained between generating enough mutations for micro-evolution to occur while maintaining fitness and genomic integrity. Pathogenic microorganisms can actively modify their mutation rate to enhance adaptive micro-evolution by increasing expression of error-prone DNA polymerases or by mutating or decreasing expression of genes required for DNA repair. Strains which exhibit an elevated mutation rate are termed mutators. Mutators are found in varying prevalence in clinical populations where large-effect beneficial mutations enhance survival and are predominately caused by defects in the DNA mismatch repair (MMR) pathway. Mutators can facilitate the emergence of antibiotic resistance, allow phenotypic modifications to prevent recognition and destruction by the host immune system and enable switching to metabolic and cellular morphologies better able to survive in the given environment. This review will focus on recent advances in understanding the phenotypic and genotypic changes occurring in MMR mutators in both prokaryotic and eukaryotic pathogens.
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20
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Riederer JM, Tiso S, van Eldijk TJ, Weissing FJ. Capturing the facets of evolvability in a mechanistic framework. Trends Ecol Evol 2022; 37:430-439. [DOI: 10.1016/j.tree.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
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21
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Love A, Wagner GP. Co-option of stress mechanisms in the origin of evolutionary novelties. Evolution 2021; 76:394-413. [PMID: 34962651 PMCID: PMC9303342 DOI: 10.1111/evo.14421] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/19/2021] [Accepted: 10/24/2021] [Indexed: 11/30/2022]
Abstract
It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress‐responsive mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co‐option of stress‐responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co‐option that identify component sources of evolutionary change, our model documents the cost‐benefit trade‐offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation.
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Affiliation(s)
- Alan Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT-06520.,Yale Systems Biology Institute, West Haven, CT-06516.,Department of Evolutionary Biology, University of Vienna, Austria
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22
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Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus. Nat Commun 2021; 12:5869. [PMID: 34620872 PMCID: PMC8497519 DOI: 10.1038/s41467-021-26108-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Mutations are the source of genetic variation and the substrate for evolution. Genome-wide mutation rates appear to be affected by selection and are probably adaptive. Mutation rates are also known to vary along genomes, possibly in response to epigenetic modifications, but causality is only assumed. In this study we determine the direct impact of epigenetic modifications and temperature stress on mitotic mutation rates in a fungal pathogen using a mutation accumulation approach. Deletion mutants lacking epigenetic modifications confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate. Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate 15-fold resulting in significantly less TE mobilization. Also accessory chromosomes have significantly higher mutation rates. Finally, we find that temperature stress substantially elevates the mutation rate. Taken together, we find that epigenetic modifications and environmental conditions modify the rate and the location of spontaneous mutations in the genome and alter its evolutionary trajectory.
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23
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Zhou W, Li Y, Li Z, Ma B, Jiang X, Hu C, Ai Y, Luo P. Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing. Front Microbiol 2021; 12:710262. [PMID: 34671325 PMCID: PMC8521149 DOI: 10.3389/fmicb.2021.710262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages (phages) and their bacterial hosts were the most abundant and genetically highly diverse organisms on the earth. In this study, a series of phage-resistant mutant (PRM) strains derived from Vibrio alginolyticus were isolated and Infrequent-restriction-site PCR (IRS-PCR) was used to investigate the genetic diversity of the PRM strains. Phenotypic variations of eight PRM strains were analyzed using profiles of utilizing carbon sources and chemical sensitivity. Genetic variations of eight PRM strains and coevolved V. alginolyticus populations with phages were analyzed by whole-genome sequencing and resequencing, respectively. The results indicated that eight genetically discrepant PRM stains exhibited abundant and abundant phenotypic variations. Eight PRM strains and coevolved V. alginolyticus populations (VE1, VE2, and VE3) contained numerous single nucleotide variations (SNVs) and insertions/indels (InDels) and exhibited obvious genetic divergence. Most of the SNVs and InDels in coding genes were related to the synthesis of flagellar, extracellular polysaccharide (EPS), which often served as the receptors of phage invasion. The PRM strains and the coevolved cell populations also contained frequent mutations in tRNA and rRNA genes. Two out of three coevolved populations (VE1 and VE2) contained a large mutation segment severely deconstructing gene nrdA, which was predictably responsible for the booming of mutation rate in the genome. In summary, numerous mutations and genetic divergence were detected in the genomes of V. alginolyticus PRM strains and in coevolved cell populations of V. alginolyticus under phage infection stress. The phage infection stress may provide an important force driving genomic evolution of V. alginolyticus.
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Affiliation(s)
- Wenjie Zhou
- College of Animal Science, Jilin University, Changchun, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yingying Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Geological Survey Institute of Guangzhou, Guangzhou, China
| | - Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yongxing Ai
- College of Animal Science, Jilin University, Changchun, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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24
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Korry BJ, Lee SYE, Chakrabarti AK, Choi AH, Ganser C, Machan JT, Belenky P. Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis. Antimicrob Agents Chemother 2021; 65:e0089121. [PMID: 34339280 PMCID: PMC8448107 DOI: 10.1128/aac.00891-21] [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: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mutagenesis is integral for bacterial evolution and the development of antibiotic resistance. Environmental toxins and stressors are known to elevate the rate of mutagenesis through direct DNA toxicity, known as stress-associated mutagenesis, or via a more general stress-induced process that relies on intrinsic bacterial pathways. Here, we characterize the spectra of mutations induced by an array of different stressors using high-throughput sequencing to profile thousands of spectinomycin-resistant colonies of Bacillus subtilis. We found 69 unique mutations in the rpsE and rpsB genes, and that each stressor leads to a unique and specific spectrum of antibiotic-resistance mutations. While some mutations clearly reflected the DNA damage mechanism of the stress, others were likely the result of a more general stress-induced mechanism. To determine the relative fitness of these mutants under a range of antibiotic selection pressures, we used multistrain competitive fitness experiments and found an additional landscape of fitness and resistance. The data presented here support the idea that the environment in which the selection is applied (mutagenic stressors that are present), as well as changes in local drug concentration, can significantly alter the path to spectinomycin resistance in B. subtilis.
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Affiliation(s)
- Benjamin J. Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Stella Ye Eun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Amit K. Chakrabarti
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Ashley H. Choi
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Collin Ganser
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jason T. Machan
- Department of Orthopedics, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Surgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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25
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Shen S, Vagner S, Robert C. Persistent Cancer Cells: The Deadly Survivors. Cell 2021; 183:860-874. [PMID: 33186528 DOI: 10.1016/j.cell.2020.10.027] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 10/15/2020] [Indexed: 02/09/2023]
Abstract
Persistent cancer cells are the discrete and usually undetected cells that survive cancer drug treatment and constitute a major cause of treatment failure. These cells are characterized by their slow proliferation, highly flexible energy consumption, adaptation to their microenvironment, and phenotypic plasticity. Mechanisms that underlie their persistence offer highly coveted and sought-after therapeutic targets, and include diverse epigenetic, transcriptional, and translational regulatory processes, as well as complex cell-cell interactions. Although the successful clinical targeting of persistent cancer cells remains to be realized, immense progress has been made in understanding their persistence, yielding promising preclinical results.
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Affiliation(s)
- Shensi Shen
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France; Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France.
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France; Université Paris-Sud, Université Paris-Saclay, Kremlin-Bicêtre, France; Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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26
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Souque C, Escudero JA, MacLean RC. Integron activity accelerates the evolution of antibiotic resistance. eLife 2021; 10:62474. [PMID: 33634790 PMCID: PMC8024014 DOI: 10.7554/elife.62474] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to 'evolve on demand' in response to antibiotic pressure. To test this hypothesis, we inserted a custom three-cassette integron into Pseudomonas aeruginosa and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.
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Affiliation(s)
- Célia Souque
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - José Antonio Escudero
- University of Oxford, Department of Zoology, Oxford, United Kingdom.,Universidad Complutense de Madrid, Departamento de Sanidad Animal and VISAVET, Madrid, Spain
| | - R Craig MacLean
- University of Oxford, Department of Zoology, Oxford, United Kingdom
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27
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Tagel M, Ilves H, Leppik M, Jürgenstein K, Remme J, Kivisaar M. Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp. Microorganisms 2020; 9:microorganisms9010025. [PMID: 33374637 PMCID: PMC7822408 DOI: 10.3390/microorganisms9010025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudouridines are known to be important for optimal translation. In this study we demonstrate an unexpected link between pseudouridylation of tRNA and mutation frequency in Pseudomonas species. We observed that the lack of pseudouridylation activity of pseudouridine synthases TruA or RluA elevates the mutation frequency in Pseudomonas putida 3 to 5-fold. The absence of TruA but not RluA elevates mutation frequency also in Pseudomonas aeruginosa. Based on the results of genetic studies and analysis of proteome data, the mutagenic effect of the pseudouridylation deficiency cannot be ascribed to the involvement of error-prone DNA polymerases or malfunctioning of DNA repair pathways. In addition, although the deficiency in TruA-dependent pseudouridylation made P. putida cells more sensitive to antimicrobial compounds that may cause oxidative stress and DNA damage, cultivation of bacteria in the presence of reactive oxygen species (ROS)-scavenging compounds did not eliminate the mutator phenotype. Thus, the elevated mutation frequency in the absence of tRNA pseudouridylation could be the result of a more specific response or, alternatively, of a cumulative effect of several small effects disturbing distinct cellular functions, which remain undetected when studied independently. This work suggests that pseudouridines link the translation machinery to mutation frequency.
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Affiliation(s)
- Mari Tagel
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | | | | | | | - Jaanus Remme
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | - Maia Kivisaar
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
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28
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Zheng J, Guo N, Wagner A. Selection enhances protein evolvability by increasing mutational robustness and foldability. Science 2020; 370:370/6521/eabb5962. [DOI: 10.1126/science.abb5962] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/25/2020] [Indexed: 01/14/2023]
Abstract
Natural selection can promote or hinder a population’s evolvability—the ability to evolve new and adaptive phenotypes—but the underlying mechanisms are poorly understood. To examine how the strength of selection affects evolvability, we subjected populations of yellow fluorescent protein to directed evolution under different selection regimes and then evolved them toward the new phenotype of green fluorescence. Populations under strong selection for the yellow phenotype evolved the green phenotype most rapidly. They did so by accumulating mutations that increase both robustness to mutations and foldability. Under weak selection, neofunctionalizing mutations rose to higher frequency at first, but more frequent deleterious mutations undermined their eventual success. Our experiments show how selection can enhance evolvability by enhancing robustness and create the conditions necessary for evolutionary success.
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Affiliation(s)
- Jia Zheng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
| | - Ning Guo
- Zwirnereistrasse 11, Wallisellen, Zurich, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
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29
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Understanding gradients in industrial bioreactors. Biotechnol Adv 2020; 46:107660. [PMID: 33221379 DOI: 10.1016/j.biotechadv.2020.107660] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 11/14/2020] [Indexed: 01/07/2023]
Abstract
Gradients in industrial bioreactors have attracted substantial research attention since exposure to fluctuating environmental conditions has been shown to lead to changes in the metabolome, transcriptome as well as population heterogeneity in industrially relevant microorganisms. Such changes have also been found to impact key process parameters like the yield on substrate and the productivity. Hence, understanding gradients is important from both the academic and industrial perspectives. In this review the causes of gradients are outlined, along with their impact on microbial physiology. Quantifying the impact of gradients requires a detailed understanding of both fluid flow inside industrial equipment and microbial physiology. This review critically examines approaches used to investigate gradients including large-scale experimental work, computational methods and scale-down approaches. Avenues for future work have been highlighted, particularly the need for further coordinated development of both in silico and experimental tools which can be used to further the current understanding of gradients in industrial equipment.
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30
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The evolution of bacterial pathogens in the Anthropocene. INFECTION GENETICS AND EVOLUTION 2020; 86:104611. [PMID: 33130070 DOI: 10.1016/j.meegid.2020.104611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022]
Abstract
Humankind has become a primary driver of global environmental and climate change. The extent of planetary change is such that it has been proposed to classify the current geological age as the 'Anthropocene'. Anthropogenic environmental degradation presents numerous threats to human health and wellbeing, including an increased risk of infectious disease. This review focuses on how processes such as pollution, climate change and human-mediated dispersal could affect the evolution of bacterial pathogens. Effects of environmental change on the 'big five' of evolution: mutation rate, recombination (horizontal gene transfer), migration, selection and drift are discussed. Microplastic pollution is used as a case study to highlight the combined effects of some of these processes on the evolutionary diversification of human pathogens. Although the evidence is still incomplete, a picture is emerging that environmental pathogens could evolve at increased rates in the Anthropocene, with potential consequences for human infection.
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31
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Ethanol exposure increases mutation rate through error-prone polymerases. Nat Commun 2020; 11:3664. [PMID: 32694532 PMCID: PMC7374746 DOI: 10.1038/s41467-020-17447-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
Ethanol is a ubiquitous environmental stressor that is toxic to all lifeforms. Here, we use the model eukaryote Saccharomyces cerevisiae to show that exposure to sublethal ethanol concentrations causes DNA replication stress and an increased mutation rate. Specifically, we find that ethanol slows down replication and affects localization of Mrc1, a conserved protein that helps stabilize the replisome. In addition, ethanol exposure also results in the recruitment of error-prone DNA polymerases to the replication fork. Interestingly, preventing this recruitment through mutagenesis of the PCNA/Pol30 polymerase clamp or deleting specific error-prone polymerases abolishes the mutagenic effect of ethanol. Taken together, this suggests that the mutagenic effect depends on a complex mechanism, where dysfunctional replication forks lead to recruitment of error-prone polymerases. Apart from providing a general mechanistic framework for the mutagenic effect of ethanol, our findings may also provide a route to better understand and prevent ethanol-associated carcinogenesis in higher eukaryotes. Whereas the toxic effects of ethanol are well-documented, the underlying mechanism is obscure. This study uses the eukaryotic model S. cerevisiae to reveal how exposure to sublethal ethanol concentrations causes DNA replication stress and an increased mutation rate.
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32
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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33
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Yi X, Kazlauskas R, Travisano M. Evolutionary innovation using EDGE, a system for localized elevated mutagenesis. PLoS One 2020; 15:e0232330. [PMID: 32353078 PMCID: PMC7192385 DOI: 10.1371/journal.pone.0232330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
Mutations arising across the whole genome can hinder the emergence of evolutionary innovation required for adaptation because many mutations are deleterious. This trade-off is overcome by elevated mutagenesis to localized loci. Examples include phase variation and diversity-generating retroelements. However, these mechanisms are rare in nature; and all have narrow mutational spectra limiting evolutionary innovation. Here, we engineer a platform of Experimental Designed Genic Evolution (EDGE) to study the potential for evolutionary novelty at a single locus. Experimental evolution with EDGE shows that bacterial resistance to a novel antibiotic readily evolves, provided that elevated mutagenesis is focused on a relevant gene. A model is proposed to account for the cost and benefit of such single loci to adaptation in a changing environment and explains their high mutation rates, limited innovation, and the rarity of localized mutagenesis in nature. Overall, our results suggest that localized mutation systems can facilitate continuing adaptive evolution without necessarily restricting the spectrum of mutations. EDGE has utility in dissecting the complex process of adaptation with its localized, efficient evolution.
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Affiliation(s)
- Xiao Yi
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Romas Kazlauskas
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michael Travisano
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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34
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New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies. Sci Rep 2019; 9:16444. [PMID: 31712730 PMCID: PMC6848147 DOI: 10.1038/s41598-019-52832-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Pseudoalteromonas haloplanktis TAC125 is among the most commonly studied bacteria adapted to cold environments. Aside from its ecological relevance, P. haloplanktis has a potential use for biotechnological applications. Due to its importance, we decided to take advantage of next generation sequencing (Illumina) and third generation sequencing (PacBio and Oxford Nanopore) technologies to resequence its genome. The availability of a reference genome, obtained using whole genome shotgun sequencing, allowed us to study and compare the results obtained by the different technologies and draw useful conclusions for future de novo genome assembly projects. We found that assembly polishing using Illumina reads is needed to achieve a consensus accuracy over 99.9% when using Oxford Nanopore sequencing, but not in PacBio sequencing. However, the dependency of consensus accuracy on coverage is lower in Oxford Nanopore than in PacBio, suggesting that a cost-effective solution might be the use of low coverage Oxford Nanopore sequencing together with Illumina reads. Despite the differences in consensus accuracy, all sequencing technologies revealed the presence of a large plasmid, pMEGA, which was undiscovered until now. Among the most interesting features of pMEGA is the presence of a putative error-prone polymerase regulated through the SOS response. Aside from the characterization of the newly discovered plasmid, we confirmed the sequence of the small plasmid pMtBL and uncovered the presence of a potential partitioning system. Crucially, this study shows that the combination of next and third generation sequencing technologies give us an unprecedented opportunity to characterize our bacterial model organisms at a very detailed level.
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35
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Abstract
In evolutionary biology, it is generally assumed that evolution occurs in the weak mutation limit, that is, the frequency of multiple mutations simultaneously occurring in the same genome and the same generation is negligible. We employ mathematical modeling to show that, although under the typical parameter values of the evolutionary process the probability of multimutational leaps is indeed low, they might become substantially more likely under stress, when the mutation rate is dramatically elevated. We hypothesize that stress-induced mutagenesis in microbes is an evolvable adaptive strategy. Multimutational leaps might matter also in other cases of substantially increased mutation rate, such as growing tumors or evolution of primordial replicators. Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multimutation leaps, that is, several mutations occurring simultaneously, within a single generation in 1 genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multimutation leap is low, and accordingly the contribution of such leaps is minor at best. However, we show that, taking sign epistasis into account, leaps could become an important factor of evolution in cases of substantially elevated mutation rates, such as stress-induced mutagenesis in microbes. We hypothesize that stress-induced mutagenesis is an evolvable adaptive strategy.
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36
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Li Z, Bock R. Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection. Nucleic Acids Res 2019; 47:6351-6359. [PMID: 31106341 PMCID: PMC6614815 DOI: 10.1093/nar/gkz370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/07/2019] [Accepted: 04/30/2019] [Indexed: 12/02/2022] Open
Abstract
Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.
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Affiliation(s)
- Zhichao Li
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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37
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Gilbert MJ, Duim B, Zomer AL, Wagenaar JA. Living in Cold Blood: Arcobacter, Campylobacter, and Helicobacter in Reptiles. Front Microbiol 2019; 10:1086. [PMID: 31191467 PMCID: PMC6530492 DOI: 10.3389/fmicb.2019.01086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.
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Affiliation(s)
- Maarten J Gilbert
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Reptile, Amphibian and Fish Conservation Netherlands, Nijmegen, Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
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38
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Liu H, Zhang J. Yeast Spontaneous Mutation Rate and Spectrum Vary with Environment. Curr Biol 2019; 29:1584-1591.e3. [PMID: 31056389 DOI: 10.1016/j.cub.2019.03.054] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 12/11/2022]
Abstract
Mutation is the ultimate genetic source of evolution and biodiversity, but to what extent the environment impacts mutation rate and spectrum is poorly understood. Past studies discovered mutagenesis induced by antibiotic treatment or starvation, but its relevance and importance to long-term evolution is unclear because these severe stressors typically halt cell growth and/or cause substantial cell deaths. Here, we quantify the mutation rate and spectrum in Saccharomyces cerevisiae by whole-genome sequencing following mutation accumulation in each of seven environments with relatively rapid cell growths and minimal cell deaths. We find the point mutation rate per generation to differ by 3.6-fold among the seven environments, generally increasing in environments with slower cell growths. This trend renders the mutation rate per year more constant than that per generation across environments, which has implications for neutral evolution and the molecular clock. Additionally, we find substantial among-environment variations in mutation spectrum, such as the transition to transversion ratio and AT mutational bias. Other main mutation types, including small insertion or deletion, segmental duplication or deletion, and chromosome gain or loss also tend to occur more frequently in environments where yeast grows more slowly. In contrast to these findings from the nuclear genome, the yeast mitochondrial mutation rate rises with the growth rate, consistent with the metabolic rate hypothesis. Together, these observations indicate that environmental changes, which are ubiquitous in nature, influence not only natural selection, but also the amount and type of mutations available to selection, and suggest that ignoring the latter impact, as is currently practiced, may mislead evolutionary inferences.
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Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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39
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Engelhardt D, Shakhnovich EI. Mutation rate variability as a driving force in adaptive evolution. Phys Rev E 2019; 99:022424. [PMID: 30934244 DOI: 10.1103/physreve.99.022424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Indexed: 11/07/2022]
Abstract
Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by selective pressure. Here we investigate the dynamics of resistance fixation in a bacterial population with variable mutation rates, and we show that evolutionary outcomes are most sensitive to mutation rate variations when the population is subject to environmental and demographic conditions that suppress the evolutionary advantage of high-fitness subpopulations. By directly mapping a biophysical fitness function to the system-level dynamics of the population, we show that both low and very high, but not intermediate, levels of stress in the form of an antibiotic result in a disproportionate effect of hypermutation on resistance fixation. We demonstrate how this behavior is directly tied to the extent of genetic hitchhiking in the system, the propagation of high-mutation rate cells through association with high-fitness mutations. Our results indicate a substantial role for mutation rate flexibility in the evolution of antibiotic resistance under conditions that present a weak advantage over wildtype to resistant cells.
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Affiliation(s)
- Dalit Engelhardt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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40
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García-Jiménez C, Goding CR. Starvation and Pseudo-Starvation as Drivers of Cancer Metastasis through Translation Reprogramming. Cell Metab 2019; 29:254-267. [PMID: 30581118 PMCID: PMC6365217 DOI: 10.1016/j.cmet.2018.11.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Considerable progress has been made in identifying microenvironmental signals that effect the reversible phenotypic transitions underpinning the early steps in the metastatic cascade. However, although the general principles underlying metastatic dissemination have been broadly outlined, a common theme that unifies many of the triggers of invasive behavior in tumors has yet to emerge. Here we discuss how many diverse signals that induce invasion converge on the reprogramming of protein translation via phosphorylation of eIF2α, a hallmark of the starvation response. These include starvation as a consequence of nutrient or oxygen limitation, or pseudo-starvation imposed by cell-extrinsic microenvironmental signals or by cell-intrinsic events, including oncogene activation. Since in response to resource limitation single-cell organisms undergo phenotypic transitions remarkably similar to those observed within tumors, we propose that a starvation/pseudo-starvation model to explain cancer progression provides an integrated and evolutionarily conserved conceptual framework to understand the progression of this complex disease.
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Affiliation(s)
- Custodia García-Jiménez
- Area de Fisiología, Facultad de CC de la Salud, Universidad Rey Juan Carlos, Avenida Atenas s/n, Alcorcón, Madrid 28922, Spain
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Old Road Campus, Headington, Oxford OX3 7DQ, UK.
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41
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Kigel N, Melnik I, Naumenko O. STUDY OF THE BIOTECHNOLOGICAL POTENTIAL OF SELECTED LACTIC ACID BACTERIA CULTURES. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.15673/fst.v12i4.1176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fermenting microflora has been selected by biotechnological activity markers, with various methodological approaches used, namely: directional selection, selection of bacteriophage-insensitive mutants, protoplast regeneration. The experimental data show a significant biotechnological potential of the selected lactic acid bacteria. They are characterized by high milk-clotting activity and yield, the ability to form aromatic compounds and/or viscous components, excellent organoleptic qualities of clots fermented by them, antago-nistic activity against pathogenic and opportunistic pathogenic microorganisms, and phage-resistance to species-specific virulent phages. The collection of industrial microorganisms of Institute of Food Resources of National Academy of Agrarian Sciences (IFR NAAS) has been supplemented with new bioactive strains, in particular, the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactoba-cillus rhamnosus and Lactococcus lactis. Four bacterial compositions have been created. Three of them (Iprovit-LB-R; Iprovit-LB-A, and Iprovit-ST) are supposed to be used as functional enrichers for dry foodstuffs or as biologically active supplements. The bacterial prepara-tion Iprovit-Bifidolux is a universal composition. It can be introduced both as a fermenting culture for milk fermentation and as an enricher for dry and liquid foodstuffs. Biotechnologies for the production of dry bacterial preparations on the basis of selected strains have been field-proven at the State Research Enterprise of Starter Cultures that belongs to the IFR NAAS. The data on a wide range of clinical and therapeutic effects of the bacterial preparation Iprovit-Bifidolux allow recommending it for manufacturing functional foods.
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Fitness and Genomic Consequences of Chronic Exposure to Low Levels of Copper and Nickel in Daphnia pulex Mutation Accumulation Lines. G3-GENES GENOMES GENETICS 2019; 9:61-71. [PMID: 30389796 PMCID: PMC6325897 DOI: 10.1534/g3.118.200797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays. After over 100 generations of mutation accumulation, we found no effects of metal exposure on the rates of single nucleotide mutations and of loss of heterozygosity events, the two mutation classes that occurred in sufficient numbers to allow statistical analysis. Similarly, rates of decline in fitness, as measured by intrinsic rate of population increase and of body size at first reproduction, were negligibly affected by metal exposure. We can reject the possibility that Daphnia were insufficiently stressed to invoke genetic responses as we have previously shown rates of large-scale deletions and duplications are elevated under metal exposure in this experiment. Overall, the mutation accumulation lines did not significantly depart from initial values for phenotypic traits measured, indicating the lineage used was broadly mutationally robust. Taken together, these results indicate that the mutagenic effects of chronic low-level exposure to these metals are restricted to certain mutation classes and that fitness consequences are likely minor and therefore unlikely to be relevant in determining the evolutionary responses of populations exposed to these stressors.
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Krašovec R, Richards H, Gifford DR, Belavkin RV, Channon A, Aston E, McBain AJ, Knight CG. Opposing effects of final population density and stress on Escherichia coli mutation rate. THE ISME JOURNAL 2018; 12:2981-2987. [PMID: 30087411 PMCID: PMC6230470 DOI: 10.1038/s41396-018-0237-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 11/14/2022]
Abstract
Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis-SIM) and decrease at high final population density (density-associated mutation-rate plasticity-DAMP). We hypothesised that these two forms of mutation-rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on error-prone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides). The combination of DAMP and SIM results in a mutation rate minimum at intermediate nutrient levels (which can support 7 × 108 cells ml-1). These findings demonstrate a strikingly close and nuanced relationship of ecological factors-stress and population density-with mutation, the fuel of all evolution.
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Affiliation(s)
- Rok Krašovec
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK.
- Faculty of Science and Engineering, The University of Manchester, Manchester, M13 9PT, UK.
| | - Huw Richards
- Faculty of Science and Engineering, The University of Manchester, Manchester, M13 9PT, UK
| | - Danna R Gifford
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Faculty of Science and Engineering, The University of Manchester, Manchester, M13 9PT, UK
| | - Roman V Belavkin
- School of Engineering and Information Sciences, Middlesex University, London, NW4 4BT, UK
| | - Alastair Channon
- School of Computing and Mathematics, Keele University, Keele, ST5 5BG, UK
| | - Elizabeth Aston
- School of Computing and Mathematics, Keele University, Keele, ST5 5BG, UK
| | - Andrew J McBain
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher G Knight
- Faculty of Science and Engineering, The University of Manchester, Manchester, M13 9PT, UK.
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Chen M, Xie S. Therapeutic targeting of cellular stress responses in cancer. Thorac Cancer 2018; 9:1575-1582. [PMID: 30312004 PMCID: PMC6275842 DOI: 10.1111/1759-7714.12890] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 11/30/2022] Open
Abstract
Similar to bacteria, yeast, and other organisms that have evolved pathways to respond to environmental stresses, cancer cells develop mechanisms that increase genetic diversity to facilitate adaptation to a variety of stressful conditions, including hypoxia, nutrient deprivation, exposure to DNA-damaging agents, and immune responses. To survive, cancer cells trigger mechanisms that drive genomic instability and mutation, alter gene expression programs, and reprogram the metabolic pathways to evade growth inhibition signaling and immune surveillance. A deeper understanding of the molecular mechanisms that underlie the pathways used by cancer cells to overcome stresses will allow us to develop more efficacious strategies for cancer therapy. Herein, we overview several key stresses imposed on cancer cells, including oxidative, metabolic, mechanical, and genotoxic, and discuss the mechanisms that drive cancer cell responses. The therapeutic implications of these responses are also considered, as these factors pave the way for the targeting of stress adaption pathways in order to slow cancer progression and block resistance to therapy.
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Affiliation(s)
- Miao Chen
- College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical SciencesShandong Normal UniversityJinanChina
| | - Songbo Xie
- College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical SciencesShandong Normal UniversityJinanChina
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Kristensen TN, Ketola T, Kronholm I. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 2018; 1476:5-22. [PMID: 30259990 DOI: 10.1111/nyas.13974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 08/24/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Environments are changing rapidly, and to cope with these changes, organisms have to adapt. Adaptation can take many shapes and occur at different speeds, depending on the type of response, the trait, the population, and the environmental conditions. The biodiversity crisis that we are currently facing illustrates that numerous species and populations are not capable of adapting with sufficient speed to ongoing environmental changes. Here, we discuss current knowledge on the ability of animals and plants to adapt to environmental stress on different timescales, mainly focusing on thermal stress and ectotherms. We discuss within-generation responses that can be fast and induced within minutes or hours, evolutionary adaptations that are often slow and take several generations, and mechanisms that lay somewhere in between and that include epigenetic transgenerational effects. To understand and predict the impacts of environmental change and stress on biodiversity, we suggest that future studies should (1) have an increased focus on understanding the type and speed of responses to fast environmental changes; (2) focus on the importance of environmental fluctuations and the predictability of environmental conditions on adaptive capabilities, preferably in field studies encompassing several fitness components; and (3) look at ecosystem responses to environmental stress and their resilience when disturbed.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | - Tarmo Ketola
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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Fungal Resistance to Echinocandins and the MDR Phenomenon in Candida glabrata. JOURNAL OF FUNGI (BASEL, SWITZERLAND) 2018; 4:jof4030105. [PMID: 30200517 PMCID: PMC6162769 DOI: 10.3390/jof4030105] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 12/17/2022]
Abstract
Candida glabrata has thoroughly adapted to successfully colonize human mucosal membranes and survive in vivo pressures. prior to and during antifungal treatment. Out of all the medically relevant Candida species, C. glabrata has emerged as a leading cause of azole, echinocandin, and multidrug (MDR: azole + echinocandin) adaptive resistance. Neither mechanism of resistance is intrinsic to C. glabrata, since stable genetic resistance depends on mutation of drug target genes, FKS1 and FKS2 (echinocandin resistance), and a transcription factor, PDR1, which controls expression of major drug transporters, such as CDR1 (azole resistance). However, another hallmark of C. glabrata is the ability to withstand drug pressure both in vitro and in vivo prior to stable "genetic escape". Additionally, these resistance events can arise within individual patients, which underscores the importance of understanding how this fungus is adapting to its environment and to drug exposure in vivo. Here, we explore the evolution of echinocandin resistance as a multistep model that includes general cell stress, drug adaptation (tolerance), and genetic escape. The extensive genetic diversity reported in C. glabrata is highlighted.
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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Shimansky YP. Trans-algorithmic nature of learning in biological systems. BIOLOGICAL CYBERNETICS 2018; 112:357-368. [PMID: 29721604 DOI: 10.1007/s00422-018-0757-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/14/2018] [Indexed: 06/08/2023]
Abstract
Learning ability is a vitally important, distinctive property of biological systems, which provides dynamic stability in non-stationary environments. Although several different types of learning have been successfully modeled using a universal computer, in general, learning cannot be described by an algorithm. In other words, algorithmic approach to describing the functioning of biological systems is not sufficient for adequate grasping of what is life. Since biosystems are parts of the physical world, one might hope that adding some physical mechanisms and principles to the concept of algorithm could provide extra possibilities for describing learning in its full generality. However, a straightforward approach to that through the so-called physical hypercomputation so far has not been successful. Here an alternative approach is proposed. Biosystems are described as achieving enumeration of possible physical compositions though random incremental modifications inflicted on them by active operating resources (AORs) in the environment. Biosystems learn through algorithmic regulation of the intensity of the above modifications according to a specific optimality criterion. From the perspective of external observers, biosystems move in the space of different algorithms driven by random modifications imposed by the environmental AORs. A particular algorithm is only a snapshot of that motion, while the motion itself is essentially trans-algorithmic. In this conceptual framework, death of unfit members of a population, for example, is viewed as a trans-algorithmic modification made in the population as a biosystem by environmental AORs. Numerous examples of AOR utilization in biosystems of different complexity, from viruses to multicellular organisms, are provided.
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Affiliation(s)
- Yury P Shimansky
- Arizona State University, Phoenix, AZ, 85004, USA.
- St. Joseph's Hospital, Phoenix, AZ, 85013, USA.
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Real-time dynamics of mutagenesis reveal the chronology of DNA repair and damage tolerance responses in single cells. Proc Natl Acad Sci U S A 2018; 115:E6516-E6525. [PMID: 29941584 DOI: 10.1073/pnas.1801101115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Evolutionary processes are driven by diverse molecular mechanisms that act in the creation and prevention of mutations. It remains unclear how these mechanisms are regulated because limitations of existing mutation assays have precluded measuring how mutation rates vary over time in single cells. Toward this goal, I detected nascent DNA mismatches as a proxy for mutagenesis and simultaneously followed gene expression dynamics in single Escherichia coli cells using microfluidics. This general microscopy-based approach revealed the real-time dynamics of mutagenesis in response to DNA alkylation damage and antibiotic treatments. It also enabled relating the creation of DNA mismatches to the chronology of the underlying molecular processes. By avoiding population averaging, I discovered cell-to-cell variation in mutagenesis that correlated with heterogeneity in the expression of alternative responses to DNA damage. Pulses of mutagenesis are shown to arise from transient DNA repair deficiency. Constitutive expression of DNA repair pathways and induction of damage tolerance by the SOS response compensate for delays in the activation of inducible DNA repair mechanisms, together providing robustness against the toxic and mutagenic effects of DNA alkylation damage.
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50
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Gibson B, Wilson DJ, Feil E, Eyre-Walker A. The distribution of bacterial doubling times in the wild. Proc Biol Sci 2018; 285:20180789. [PMID: 29899074 PMCID: PMC6015860 DOI: 10.1098/rspb.2018.0789] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/18/2018] [Indexed: 12/16/2022] Open
Abstract
Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.
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Affiliation(s)
- Beth Gibson
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Edward Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
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