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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [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: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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Sequence Polymorphisms in Vibrio cholerae HapR Affect Biofilm Formation under Aerobic and Anaerobic Conditions. Appl Environ Microbiol 2022; 88:e0104422. [PMID: 35969071 PMCID: PMC9469714 DOI: 10.1128/aem.01044-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the influence of hapR sequence mutations on the biofilm formation of Vibrio cholerae. In this study, hapR sequences from 85 V. cholerae strains belonging to both pandemic and nonpandemic serogroup were investigated through phylogenetic and sequence analyses. Biofilm formation assays under aerobic and anaerobic conditions were also performed. Sequence variations include single point mutations and insertions/deletions (indels) leading to either truncated or frameshifted HapR. Population structure analysis revealed two major hapR haplogroups, hapR1 and hapR2. Phylogenetic reconstruction displayed a hypothetical ancestral hapR sequence located within the hapR1 haplogroup. Higher numbers of single nucleotide polymorphisms and genetic diversity indices were observed in hapR1, while indels occurred dominantly in hapR2. Aerobic conditions supported more robust biofilms compared to anaerobic conditions. Strains with frameshifted HapR produced the largest amount of biofilm under both oxygen conditions. Quantitative real-time PCR assay confirmed that strains with truncated and frameshifted HapR resulted in a nonfunctional regulator as exhibited by the significantly low hapA gene expression. The present study shows that HapR mutations had a strong influence on biofilm formation and that sequence polymorphisms leading to the disruption of DNA-binding sites or dimerization of the HapR will result in more-robust V. cholerae biofilms. IMPORTANCE Our study revealed an ancestral hapR sequence from a phylogenetic reconstruction that displayed the evolutionary lineage of the nonpandemic to the pandemic strains. Here, we established hapR1 and hapR2 as major hapR haplogroups. The association of the O1 and O139 serogroups with the hapR2 haplogroup demonstrated the distinction of hapR2 in causing cholera infection. Moreover, mutations in this regulator that could lead to the disruption of transcription factor-binding sites or dimerization of the HapR can significantly affect the biofilm formation of V. cholerae. These observations on the relationship of the hapR polymorphism and V. cholerae biofilm formation will provide additional considerations for future biofilm studies and insights into the epidemiology of the pathogen that could ultimately help in the surveillance and mitigation of future cholera disease outbreaks.
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Fogalli GB, Line SRP. Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells. J Mol Evol 2021; 89:257-268. [PMID: 33760966 DOI: 10.1007/s00239-021-10003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/10/2021] [Indexed: 11/26/2022]
Abstract
Proteins can evolve by accumulating changes on amino acid sequences. These changes are mainly caused by missense mutations on its DNA coding sequences. Mutations with neutral or positive effects on fitness can be maintained while deleterious mutations tend to be eliminated by natural selection. Amino acid changes are influenced by the biophysical, chemical, and biological properties of amino acids. There is a multiplicity of amino acid properties that can influence the function and expression of proteins. Amino acid properties can be expressed into numerical indexes, which can help to predict functional and structural aspects of proteins and allow statistical inferences of selection pressure on amino acid usage. The accuracy of these analyses may be compromised by the existence of several numerical indexes that measure the same amino acid property, and the lack of objective parameters to determine the most accurate and biologically relevant index. In the present study, the gradient consistency test was used in order to estimate the magnitude of directional selection imparted by amino acid biochemical and biophysical properties on protein evolution.
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Affiliation(s)
- Giovani B Fogalli
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Campinas, Brazil
| | - Sergio R P Line
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Campinas, Brazil.
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Miller TEX, Angert AL, Brown CD, Lee-Yaw JA, Lewis M, Lutscher F, Marculis NG, Melbourne BA, Shaw AK, Szűcs M, Tabares O, Usui T, Weiss-Lehman C, Williams JL. Eco-evolutionary dynamics of range expansion. Ecology 2020; 101:e03139. [PMID: 32697876 DOI: 10.1002/ecy.3139] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/05/2020] [Accepted: 06/08/2020] [Indexed: 01/31/2023]
Abstract
Understanding the movement of species' ranges is a classic ecological problem that takes on urgency in this era of global change. Historically treated as a purely ecological process, range expansion is now understood to involve eco-evolutionary feedbacks due to spatial genetic structure that emerges as populations spread. We synthesize empirical and theoretical work on the eco-evolutionary dynamics of range expansion, with emphasis on bridging directional, deterministic processes that favor evolved increases in dispersal and demographic traits with stochastic processes that lead to the random fixation of alleles and traits. We develop a framework for understanding the joint influence of these processes in changing the mean and variance of expansion speed and its underlying traits. Our synthesis of recent laboratory experiments supports the consistent role of evolution in accelerating expansion speed on average, and highlights unexpected diversity in how evolution can influence variability in speed: results not well predicted by current theory. We discuss and evaluate support for three classes of modifiers of eco-evolutionary range dynamics (landscape context, trait genetics, and biotic interactions), identify emerging themes, and suggest new directions for future work in a field that stands to increase in relevance as populations move in response to global change.
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Affiliation(s)
- Tom E X Miller
- Program in Ecology and Evolutionary Biology, Department of BioSciences, Rice University, Houston, Texas, 77005, USA
| | - Amy L Angert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z2, Canada
| | - Carissa D Brown
- Department of Geography, Memorial University, 230 Elizabeth Avenue, St John's, Newfoundland and Labrador, A1B 3X9, Canada
| | - Julie A Lee-Yaw
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z2, Canada.,Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Mark Lewis
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
| | - Frithjof Lutscher
- Department of Mathematics and Statistics, and Department of Biology, University of Ottawa, Ottawa, Ottawa, K1N 6N5, Canada
| | - Nathan G Marculis
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada.,Department of Environmental Science and Policy, University of California-Davis, Davis, California, 95616, USA
| | - Brett A Melbourne
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Allison K Shaw
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Marianna Szűcs
- Department of Entomology, Michigan State University, 288 Farm Lane, East Lansing, Michigan, 48824, USA
| | - Olivia Tabares
- Department of Geography and Biodiversity Research Centre, University of British Columbia, 1984 West Mall, Vancouver, British Columbia, V6T 1Z2, Canada
| | - Takuji Usui
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z2, Canada
| | - Christopher Weiss-Lehman
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Jennifer L Williams
- Department of Geography and Biodiversity Research Centre, University of British Columbia, 1984 West Mall, Vancouver, British Columbia, V6T 1Z2, Canada
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Bosshard L, Peischl S, Ackermann M, Excoffier L. Dissection of the mutation accumulation process during bacterial range expansions. BMC Genomics 2020; 21:253. [PMID: 32293258 PMCID: PMC7092555 DOI: 10.1186/s12864-020-6676-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/13/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Recent experimental work has shown that the evolutionary dynamics of bacteria expanding across space can differ dramatically from what we expect under well-mixed conditions. During spatial expansion, deleterious mutations can accumulate due to inefficient selection on the expansion front, potentially interfering with and modifying adaptive evolutionary processes. RESULTS We used whole genome sequencing to follow the genomic evolution of 10 mutator Escherichia coli lines during 39 days ( ~ 1650 generations) of a spatial expansion, which allowed us to gain a temporal perspective on the interaction of adaptive and non-adaptive evolutionary processes during range expansions. We used elastic net regression to infer the positive or negative effects of mutations on colony growth. The colony size, measured after three day of growth, decreased at the end of the experiment in all 10 lines, and mutations accumulated at a nearly constant rate over the whole experiment. We find evidence that beneficial mutations accumulate primarily at an early stage of the experiment, leading to a non-linear change of colony size over time. Indeed, the rate of colony size expansion remains almost constant at the beginning of the experiment and then decreases after ~ 12 days of evolution. We also find that beneficial mutations are enriched in genes encoding transport proteins, and genes coding for the membrane structure, whereas deleterious mutations show no enrichment for any biological process. CONCLUSIONS Our experiment shows that beneficial mutations target specific biological functions mostly involved in inter or extra membrane processes, whereas deleterious mutations are randomly distributed over the whole genome. It thus appears that the interaction between genetic drift and the availability or depletion of beneficial mutations determines the change in fitness of bacterial populations during range expansion.
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Affiliation(s)
- Lars Bosshard
- CMPG, Institute of Ecology an Evolution, University of Berne, Baltzerstrasse 6, 3012, Berne, Switzerland. .,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.,Interfaculty Bioinformatics Unit, University of Berne, 3012, Berne, Switzerland
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology Zurich (ETH Zürich), 8092, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
| | - Laurent Excoffier
- CMPG, Institute of Ecology an Evolution, University of Berne, Baltzerstrasse 6, 3012, Berne, Switzerland. .,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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Wein T, Dagan T. The Effect of Population Bottleneck Size and Selective Regime on Genetic Diversity and Evolvability in Bacteria. Genome Biol Evol 2019; 11:3283-3290. [PMID: 31688900 PMCID: PMC7145630 DOI: 10.1093/gbe/evz243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2019] [Indexed: 12/20/2022] Open
Abstract
Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity, and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. In this study, we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, and large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size; hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.
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Affiliation(s)
- Tanita Wein
- Institute of Microbiology, Kiel University, Germany
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Germany
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