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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [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] [Indexed: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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2
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Jones CT, Meynell L, Neto C, Susko E, Bielawski JP. The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations. BMC Ecol Evol 2023; 23:11. [PMID: 37046187 PMCID: PMC10100367 DOI: 10.1186/s12862-023-02112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Kin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists. Here we take a different explanatory approach based on the recently proposed concept of an "ecological scaffold". We demonstrate that ecological conditions consisting of a patchy nutrient supply that generates a metapopulation structure, episodic mixing of groups, and severe nutrient limitation, can support or "scaffold" the evolution of altruism in a population of microbes by amplifying drift. This contrasts with recent papers in which the ecological scaffold was shown to support selective processes and demonstrates the power of scaffolding even in the absence of selection. RESULTS Using computer simulations motivated by a simple theoretical model, we show that, although an altruistic mutant can be fixed within a single population of non-altruists by drift when nutrients are severely limited, the resulting altruistic population remains vulnerable to non-altruistic mutants. We then show how the imposition of the "ecological scaffold" onto a population of non-altruists alters the balance between selection and drift in a way that supports the fixation and subsequent persistence of altruism despite the possibility of invasion by non-altruists. CONCLUSIONS The fixation of an altruistic mutant by drift is possible when supported by ecological conditions that impose a metapopulation structure, episodic mixing of groups, and severe nutrient limitation. This is significant because it offers an alternative explanation for the evolution of altruism based on drift rather than selection. Given the ubiquity of low-nutrient "oligotrophic" environments in which microbes exist (e.g., the open ocean, deep subsurface soils, or under the polar ice caps) our results suggest that altruistic and cooperative behaviors may be highly prevalent among microbial populations.
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Affiliation(s)
- C T Jones
- Department of Biochemistry and Molecular Biology, Dalhousie University, NS, Halifax, Canada.
| | - L Meynell
- Department of Philosophy, Dalhousie University, Halifax, Canada
| | - C Neto
- Department of Social and Political Sciences, Philosophy, and Anthropology, University of Exeter, Exeter, UK
- Centre for the Study of the Life Sciences, EGENIS, University of Exeter, Exeter, UK
| | - E Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - J P Bielawski
- Department of Biology and Dept. of Mathematics and Statistics, Dalhousie University, Halifax, Canada
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3
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Nitschke MC, Black AJ, Bourrat P, Rainey PB. The effect of bottleneck size on evolution in nested Darwinian populations. J Theor Biol 2023; 561:111414. [PMID: 36639021 DOI: 10.1016/j.jtbi.2023.111414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/15/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
Previous work has shown how a minimal ecological structure consisting of patchily distributed resources and recurrent dispersal between patches can scaffold Darwinian properties onto collections of cells. When the timescale of dispersal is long compared with the time to consume resources, patch fitness increases but comes at a cost to cell growth rates. This creates conditions that initiate evolutionary transitions in individuality. A key feature of the scaffold is a bottleneck created during dispersal, causing patches to be founded by single cells. The bottleneck decreases competition within patches and, hence, creates a strong hereditary link at the level of patches. Here, we construct a fully stochastic model to investigate the effect of bottleneck size on the evolutionary dynamics of both cells and collectives. We show that larger bottlenecks simply slow the dynamics, but, at some point, which depends on the parameters of the within-patch model, the direction of evolution towards the equilibrium reverses. Introduction of random fluctuations in bottleneck sizes with some positive probability of smaller sizes counteracts this, even when the probability of smaller bottlenecks is minimal.
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Affiliation(s)
- Matthew C Nitschke
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.
| | - Andrew J Black
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Pierrick Bourrat
- Philosophy Department, Macquarie University, NSW 2109, Australia; Department of Philosophy and Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany; Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
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4
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Rainey PB. Major evolutionary transitions in individuality between humans and AI. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210408. [PMID: 36688400 PMCID: PMC9869444 DOI: 10.1098/rstb.2021.0408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
That humans might undergo future evolutionary transitions in individuality (ETIs) seems fanciful. However, drawing upon recent thinking concerning the origins of properties that underpin ETIs, I argue that certain ETIs are imminently realizable. Central to my argument is recognition that heritable variance in fitness at higher levels of organization can be externally imposed (scaffolded) by specific ecological structures and cultural practices. While ETIs to eusociality seem highly improbable, ETIs involving symbioses between humans and artificial intelligence (AI) can be readily envisaged. A necessary requirement is that fitness-affecting interactions between humans and AI devices are inherited by offspring. The Mendelian nature of human reproduction ensures that offspring resemble parents. Reproduction of AI devices requires nothing more than transference of algorithms from parental AI devices to devices that are assigned to offspring. This simple copying, combined with societal structures that require humans to carry AI devices, ensures heritable variance in fitness at the level of both interacting partners. Selection at the collective level will drive alignment of replicative fates and increase co-dependency, thus alleviating need for continual imposition of externally imposed scaffolds. I conclude by drawing attention to the immediacy of such transitions and express concern over possibilities for malevolent manipulation. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany,Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
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5
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Pásztor L. Population regulation and adaptive dynamics of cross-feeding. Biol Futur 2022; 73:393-403. [PMID: 36550237 DOI: 10.1007/s42977-022-00147-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
The particular importance of evolutionary studies in microbial experimental systems is that starting from the level of the metabolism of individual cells, the adaptive dynamics can be followed step by step by biochemical, genetic, and population dynamical tools. Moreover, the coincidence of evolutionary and ecological time scales helps to clarify the mutual role of ecological and evolutionary principles in predicting adaptive dynamics in general. Ecological principles define the ecological conditions under which adaptive branching can occur. This paper overviews and interprets the results of empirical and modeling studies of the evolution of metabolic cross-feeding in glucose-limited E.coli chemostats and batch cultures in the context of theories of robust coexistence and adaptive dynamics. Empirical results consistently demonstrate that the interactions between cells are mediated by the changing metabolite concentrations in the cultures and modeling confirms that these changes may control the adaptive dynamics of the clones. In consequence, the potential results of evolution can be predicted at the functional level by evolutionary flux balance analysis (evoFBA), while the genetic changes are more contingent. evoFBA follows the scheme of adaptive dynamics theory by calculating the feedback environment that changes during the evolutionary process and provides a promising tool to further investigate adaptive divergence in small microbial communities. Three general conclusions close the paper.
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Affiliation(s)
- Liz Pásztor
- School of Advanced Studies, University of Tyumen, Tyumen, 800 000, Siberia, Russia. .,Department of Genetics, Eötvös University (ELTE), Budapest, Hungary.
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6
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Deatherage DE, Barrick JE. High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. Cell Syst 2021; 12:1187-1200.e4. [PMID: 34536379 DOI: 10.1016/j.cels.2021.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/14/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Understanding how cells are likely to evolve can guide medical interventions and bioengineering efforts that must contend with unwanted mutations. The adaptome of a cell-the neighborhood of genetic changes that are most likely to drive adaptation in a given environment-can be mapped by tracking rare beneficial variants during the early stages of clonal evolution. We used multiplex adaptome capture sequencing (mAdCap-seq), a procedure that combines unique molecular identifiers and hybridization-based enrichment, to characterize mutations in eight Escherichia coli genes known to be under selection in a laboratory environment. We tracked 301 mutations at frequencies as low as 0.01% and inferred the fitness effects of 240 of these mutations. There were distinct molecular signatures of selection on protein structure and function for the three genes with the most beneficial mutations. Our results demonstrate how mAdCap-seq can be used to deeply profile a targeted portion of a cell's adaptome.
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Affiliation(s)
- Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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7
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Pentz JT, Lind PA. Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens. PLoS Genet 2021; 17:e1009722. [PMID: 34351900 PMCID: PMC8370652 DOI: 10.1371/journal.pgen.1009722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/17/2021] [Accepted: 07/16/2021] [Indexed: 11/18/2022] Open
Abstract
Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were changed compared to the SBW25 system to test if forecasts were extendable to a non-identical environment. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the Pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including an uncharacterized polysaccharide synthase operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spot sites were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.
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Affiliation(s)
| | - Peter A. Lind
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- * E-mail:
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8
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Rout UK, Sanket AS, Sisodia BS, Mohapatra PK, Pati S, Kant R, Dwivedi GR. A Comparative Review on Current and Future Drug Targets Against Bacteria & Malaria. Curr Drug Targets 2021; 21:736-775. [PMID: 31995004 DOI: 10.2174/1389450121666200129103618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 11/22/2022]
Abstract
Long before the discovery of drugs like 'antibiotic and anti-parasitic drugs', the infectious diseases caused by pathogenic bacteria and parasites remain as one of the major causes of morbidity and mortality in developing and underdeveloped countries. The phenomenon by which the organism exerts resistance against two or more structurally unrelated drugs is called multidrug resistance (MDR) and its emergence has further complicated the treatment scenario of infectious diseases. Resistance towards the available set of treatment options and poor pipeline of novel drug development puts an alarming situation. A universal goal in the post-genomic era is to identify novel targets/drugs for various life-threatening diseases caused by such pathogens. This review is conceptualized in the backdrop of drug resistance in two major pathogens i.e. "Pseudomonas aeruginosa" and "Plasmodium falciparum". In this review, the available targets and key mechanisms of resistance of these pathogens have been discussed in detail. An attempt has also been made to analyze the common drug targets of bacteria and malaria parasite to overcome the current drug resistance scenario. The solution is also hypothesized in terms of a present pipeline of drugs and efforts made by scientific community.
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Affiliation(s)
- Usha K Rout
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar-751023, India
| | | | - Brijesh S Sisodia
- Regional Ayurveda Research Institute for Drug Development, Gwalior-474 009, India
| | | | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar-751023, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh- 273013, India
| | - Gaurav R Dwivedi
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh- 273013, India
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9
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Borchert E, Hammerschmidt K, Hentschel U, Deines P. Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology. Trends Microbiol 2021; 29:908-918. [PMID: 33812769 DOI: 10.1016/j.tim.2021.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022]
Abstract
Environmental accumulation of anthropogenic pollutants is a pressing global issue. The biodegradation of these pollutants by microbes is an emerging field but is hampered by inefficient degradation rates and a limited knowledge of potential enzymes and pathways. Here, we advocate the view that significant progress can be achieved by harnessing artificial community selection for a desired biological process, an approach that makes use of eco-evolutionary principles. The selected communities can either be directly used in bioremediation applications or further be analyzed and modified, for instance through a combination of systems biology, synthetic biology, and genetic engineering. This knowledge can then inform machine learning and enhance the discovery of novel biodegradation pathways.
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Affiliation(s)
- Erik Borchert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany; University of Kiel, Kiel, Germany
| | - Peter Deines
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
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10
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Kwak GY, Goo E, Jeong H, Hwang I. Adverse effects of adaptive mutation to survive static culture conditions on successful fitness of the rice pathogen Burkholderia glumae in a host. PLoS One 2020; 15:e0238151. [PMID: 32833990 PMCID: PMC7444824 DOI: 10.1371/journal.pone.0238151] [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: 05/11/2020] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria often possess relatively flexible genome structures and adaptive genetic variants that allow survival in unfavorable growth conditions. Bacterial survival tactics in disadvantageous microenvironments include mutations that are beneficial against threats in their niche. Here, we report that the aerobic rice bacterial pathogen Burkholderia glumae BGR1 changes a specific gene for improved survival in static culture conditions. Static culture triggered formation of colony variants with deletions or point mutations in the gene bspP (BGLU_RS28885), which putatively encodes a protein that contains PDC2, PAS-9, SpoIIE, and HATPase domains. The null mutant of bspP survived longer in static culture conditions and produced a higher level of bis-(3'-5')-cyclic dimeric guanosine monophosphate than the wild type. Expression of the bacterial cellulose synthase regulator (bcsB) gene was upregulated in the mutant, consistent with the observation that the mutant formed pellicles faster than the wild type. Mature pellicle formation was observed in the bspP mutant before pellicle formation in wild-type BGR1. However, the population density of the bspP null mutant decreased substantially when grown in Luria-Bertani medium with vigorous agitation due to failure of oxalate-mediated detoxification of the alkaline environment. The bspP null mutant was less virulent and exhibited less effective colonization of rice plants than the wild type. All phenotypes caused by mutations in bspP were recovered to those of the wild type by genetic complementation. Thus, although wild-type B. glumae BGR1 prolonged viability by spontaneous mutation under static culture conditions, such genetic changes negatively affected colonization in rice plants. These results suggest that adaptive gene sacrifice of B. glumae to survive unfavorable growth conditions is not always desirable as it can adversely affect adaptability in the host.
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Affiliation(s)
- Gi-Young Kwak
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Haeyoon Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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11
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Rose CJ, Hammerschmidt K, Pichugin Y, Rainey PB. Meta‐population structure and the evolutionary transition to multicellularity. Ecol Lett 2020; 23:1380-1390. [DOI: 10.1111/ele.13570] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/27/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Caroline J. Rose
- New Zealand Institute for Advanced StudyMassey University Auckland New Zealand
| | | | - Yuriy Pichugin
- New Zealand Institute for Advanced StudyMassey University Auckland New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey University Auckland New Zealand
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12
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Doulcier G, Lambert A, De Monte S, Rainey PB. Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity. eLife 2020; 9:e53433. [PMID: 32633717 PMCID: PMC7440921 DOI: 10.7554/elife.53433] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.
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Affiliation(s)
- Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
| | - Amaury Lambert
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRSParisFrance
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERMParisFrance
| | - Silvia De Monte
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary BiologyPlönGermany
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13
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Rainey PB, Quistad SD. Toward a dynamical understanding of microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190248. [PMID: 32200735 PMCID: PMC7133524 DOI: 10.1098/rstb.2019.0248] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Abstract
The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 75231 Paris, France
| | - Steven D. Quistad
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 75231 Paris, France
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14
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Quistad SD, Doulcier G, Rainey PB. Experimental manipulation of selfish genetic elements links genes to microbial community function. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190681. [PMID: 32200751 PMCID: PMC7133536 DOI: 10.1098/rstb.2019.0681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
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Affiliation(s)
- Steven D Quistad
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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15
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Geyrhofer L, Brenner N. Coexistence and cooperation in structured habitats. BMC Ecol 2020; 20:14. [PMID: 32122337 PMCID: PMC7053132 DOI: 10.1186/s12898-020-00281-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/18/2020] [Indexed: 12/19/2022] Open
Abstract
Background Natural habitats are typically structured, imposing constraints on inhabiting populations and their interactions. Which conditions are important for coexistence of diverse communities, and how cooperative interaction stabilizes in such populations, have been important ecological and evolutionary questions. Results We investigate a minimal ecological framework of microbial population dynamics that exhibits crucial features to show coexistence: Populations repeatedly undergo cycles of separation into compartmentalized habitats and mixing with new resources. The characteristic time-scale is longer than that typical of individual growth. Using analytic approximations, averaging techniques and phase-plane methods of dynamical systems, we provide a framework for analyzing various types of microbial interactions. Population composition and population size are both dynamic variables of the model; they are found to be decoupled both in terms of time-scale and parameter dependence. We present specific results for two examples of cooperative interaction by public goods: collective antibiotics resistance, and enhanced iron-availability by pyoverdine. We find stable coexistence to be a likely outcome. Conclusions The two simple features of a long mixing time-scale and spatial compartmentalization are enough to enable coexisting strains. In particular, costly social traits are often stabilized in such an environment—and thus cooperation established.
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Affiliation(s)
- Lukas Geyrhofer
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Naama Brenner
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
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16
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Black AJ, Bourrat P, Rainey PB. Ecological scaffolding and the evolution of individuality. Nat Ecol Evol 2020; 4:426-436. [PMID: 32042121 DOI: 10.1038/s41559-019-1086-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
Abstract
Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprising patchily distributed resources and between-patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death-birth process arising from the interplay between the timing of dispersal events and the rate of resource use by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realization of evolutionary transitions.
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Affiliation(s)
- Andrew J Black
- School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Pierrick Bourrat
- Department of Philosophy, Macquarie University, Sydney, New South Wales, Australia.,Department of Philosophy & Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany. .,Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, Paris, France.
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17
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McDonald MJ. Microbial Experimental Evolution - a proving ground for evolutionary theory and a tool for discovery. EMBO Rep 2019; 20:e46992. [PMID: 31338963 PMCID: PMC6680118 DOI: 10.15252/embr.201846992] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/23/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life sciences, microbial experimental evolution has become a tool, deployed as part of the suite of techniques available to the molecular biologist. Here, I provide a review of the general findings of microbial experimental evolution, especially those relevant to molecular microbiologists that are new to the field. I also relate these results to design considerations for an evolution experiment and suggest future directions for those working at the intersection of experimental evolution and molecular biology.
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Affiliation(s)
- Michael J McDonald
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
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18
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Remigi P, Masson-Boivin C, Rocha EP. Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions. Trends Microbiol 2019; 27:623-634. [DOI: 10.1016/j.tim.2019.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
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19
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Remigi P, Ferguson GC, McConnell E, De Monte S, Rogers DW, Rainey PB. Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase. Mol Biol Evol 2019; 36:1056-1070. [PMID: 30835283 PMCID: PMC6501884 DOI: 10.1093/molbev/msz041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Observations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases, and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacterium Pseudomonas fluorescens SBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation in carB that decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a preexisting but hitherto unrecognized phenotypic switch. Genetic components surrounding bifurcation of UTP flux toward DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses-and based on a combination of genetics, transcriptomics, biochemistry, and mathematical modeling-we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a positively autoregulated activator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a program that determines stochastic entry into a semiquiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.
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Affiliation(s)
- Philippe Remigi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Laboratoire des Interactions Plantes-Microorganismes (LIPM), Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gayle C Ferguson
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Ellen McConnell
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Silvia De Monte
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David W Rogers
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris Tech), CNRS UMR 8231, PSL Research University, Paris, France
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20
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Fuqua C, Filloux A, Ghigo JM, Visick KL. Biofilms 2018: A diversity of microbes and mechanisms. J Bacteriol 2019; 201:JB.00118-19. [PMID: 30782638 PMCID: PMC6707918 DOI: 10.1128/jb.00118-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The 8th ASM Conference on Biofilms was held in Washington D.C. on October 7-11, 2018. This very highly subscribed meeting represented a wide breadth of current research in biofilms, and included over 500 attendees, 12 sessions with 64 oral presentations, and four poster sessions with about 400 posters.
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Affiliation(s)
- Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College, London, United Kingdom
| | - Jean-Marc Ghigo
- Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, Paris, France
| | - Karen L. Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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21
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Spang A, Offre P. Towards a systematic understanding of differences between archaeal and bacterial diversity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:9-12. [PMID: 30394664 PMCID: PMC7379672 DOI: 10.1111/1758-2229.12701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 06/12/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistryand Utrecht UniversityNL‐1790 ABDen BurgThe Netherlands
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123UppsalaSweden
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistryand Utrecht UniversityNL‐1790 ABDen BurgThe Netherlands
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Lind PA, Libby E, Herzog J, Rainey PB. Predicting mutational routes to new adaptive phenotypes. eLife 2019; 8:e38822. [PMID: 30616716 PMCID: PMC6324874 DOI: 10.7554/elife.38822] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive 'wrinkly spreader' (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.
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Affiliation(s)
- Peter A Lind
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Molecular BiologyUmeå UniversityUmeåSweden
| | - Eric Libby
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Santa Fe InstituteNew MexicoUnited States
- Department of MathematicsUmeå UniversityUmeåSweden
| | - Jenny Herzog
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, ESPCI Paris-TechCNRS UMR 8231, PSL Research UniversityParisFrance
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23
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Li J, Levitan B, Gomez-Jimenez S, Kültz D. Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks ( Gasterosteus aculeatus). Mol Cell Proteomics 2018; 17:2146-2163. [PMID: 30093419 PMCID: PMC6210217 DOI: 10.1074/mcp.ra118.000973] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
A data-independent acquisition (DIA) assay library for quantitative analyses of proteome dynamics has been developed for gills of threespine sticklebacks (Gasterosteus aculeatus). A raw spectral library was generated by data-dependent acquisition (DDA) and annotation of tryptic peptides to MSMS spectra and protein database identifiers. The assay library was constructed from the raw spectral library by removal of low-quality, ambiguous, and low-signal peptides. Only unique proteins represented by at least two peptides are included in the assay library, which consists of 1506 proteins, 5074 peptides, 5104 precursors, and 25,322 transitions. This assay library was used with DIA data to identify biochemical differences in gill proteomes of four populations representing different eco- and morpho-types of threespine sticklebacks. The assay library revealed unique and reproducible proteome signatures. Warm-adapted, low-plated, brackish-water fish from Laguna de la Bocana del Rosario (Mexico) show elevated HSP47, extracellular matrix, and innate immunity proteins whereas several immunoglobulins, interferon-induced proteins, ubiquitins, proteolytic enzymes, and nucleic acid remodeling proteins are reduced. Fully-plated, brackish-water fish from Westchester Lagoon (Alaska) display elevated ion regulation, GTPase signaling, and contractile cytoskeleton proteins, altered abundances of many ribosomal, calcium signaling and immunity proteins, and depleted transcriptional regulators and metabolic enzymes. Low-plated freshwater fish from Lake Solano (California) have elevated inflammasomes and proteolytic proteins whereas several iron containing and ion regulatory proteins are reduced. Gills of fully-plated, marine fish from Bodega Harbor (California) have elevated oxidative metabolism enzymes and reduced transglutaminase 2, collagens, and clathrin heavy chains. These distinct proteome signatures represent targets for testing ecological and evolutionary influences on molecular mechanisms of gill function in threespine sticklebacks. Furthermore, the gill assay library represents a model for other tissues and paves the way for accurate and reproducible network analyses of environmental context-dependent proteome dynamics in complex organisms.
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Affiliation(s)
- Johnathon Li
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616
| | - Bryn Levitan
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616
| | - Silvia Gomez-Jimenez
- §Centro de Investigación en Alimentación y Desarrollo, Carretera a la Victoria Km. 0.6, Apartado, Hermosillo, Sonora, México C.P. 83000
| | - Dietmar Kültz
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616; .,¶Coastal Marine Sciences Institute, University of California, Davis
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