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Labourel FJF, Daubin V, Menu F, Rajon E. Proteome allocation and the evolution of metabolic cross-feeding. Evolution 2024; 78:849-859. [PMID: 38376478 DOI: 10.1093/evolut/qpae008] [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: 12/27/2022] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
In a common instance of metabolic cross-feeding (MCF), an organism incompletely metabolizes nutrients and releases metabolites that are used by another to produce energy or building blocks. Why would the former waste edible food, and why does this preferentially occur at specific locations in a metabolic pathway have challenged evolutionary theory for decades. To address these questions, we combine adaptive dynamics with an explicit model of cell metabolism, including enzyme-driven catalysis of metabolic reactions and the cellular constraints acting on the proteome that may incur a cost to expressing all enzymes along a pathway. After pointing out that cells should in principle prioritize upstream reactions when metabolites are restrained inside the cell, we show that the occurrence of permeability-driven MCF is rare and requires that an intermediate metabolite be extremely diffusive. Indeed, only at very high levels of membrane permeability (consistent with those of acetate and glycerol, for instance) and under distinctive sets of parameters should the population diversify and MCF evolve. These results help understand the origins of simple microbial communities, such as those that readily evolve in short-term evolutionary experiments, and may later be extended to investigate how evolution has progressively built up today's extremely diverse ecosystems.
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Affiliation(s)
- Florian J F Labourel
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Vincent Daubin
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Frédéric Menu
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Etienne Rajon
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
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2
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Zhou K, Yi X, Tan Z, Peng M, Xiao N. Baohe pill decoction treats diarrhea induced by high-fat and high-protein diet by regulating lactase-producing bacteria in intestinal mucosa. Front Microbiol 2023; 14:1157475. [PMID: 37228379 PMCID: PMC10203203 DOI: 10.3389/fmicb.2023.1157475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction This study aimed to investigate the effects of Baohe pill decoction (BPD) on microbial, lactase activity, and lactase-producing bacteria in the intestinal mucosa of mice with diarrhea induced by high-fat and high-protein diet (HFHPD). Methods Thirty male Kunming (KM) mice were randomly divided into normal (NM), model (MD), and BPD groups. Diarrhea models were manufactured using HFHPD combined with a gavage of vegetable oil. At the end of modeling, the BPD group was given BPD (6.63 g·kg-1d-1) intervention twice daily for 3 d. The NM and MD groups were given equal amounts of sterile water. Subsequently, the intestinal mucosa of the mice was collected, one portion was used for microbial and lactase activity measurement, and the other portion was used for its lactase-producing bacterial characteristics by high-throughput sequencing technology. Results Our results showed that microbial and lactase activity of intestinal mucosa decreased significantly following diarrhea in mice (Pmicrobial < 0.05, Plactase < 0.001). After BPD intervention, microbial and lactase activity increased significantly (P < 0.01). The number of operational taxonomic units (OTUs), richness, and diversity index of lactase-producing bacteria increased in the BPD group compared to the MD group (P > 0.05), and the community structure were significant differences (P < 0.01). Compared to other groups, Saccharopolyspora, Rhizobium, Cedecea, and Escherichia were enriched in the BPD group. Notably, the relative abundance of the dominant lactase-producing genus Bifidobacterium decreased after BPD intervention. Discussion The mechanism of BPD in relieving diarrhea induced by HFHPD is closely related to the promotion of lactase activity in the intestinal mucosa, which may be achieved by regulating the structure of lactase-producing bacteria.
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Affiliation(s)
- Kang Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Xin Yi
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Zhoujin Tan
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Maijiao Peng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Nenqun Xiao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
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3
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Dal Co A, Ackermann M, van Vliet S. Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals. Cell Syst 2023; 14:98-108. [PMID: 36796335 DOI: 10.1016/j.cels.2022.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.
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Affiliation(s)
- Alma Dal Co
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Duebendorf, Switzerland.
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Colizzi ES, Hogeweg P, Vroomans RMA. Modelling the evolution of novelty: a review. Essays Biochem 2022; 66:727-735. [PMID: 36468669 PMCID: PMC9750852 DOI: 10.1042/ebc20220069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
Evolution has been an inventive process since its inception, about 4 billion years ago. It has generated an astounding diversity of novel mechanisms and structures for adaptation to the environment, for competition and cooperation, and for organisation of the internal and external dynamics of the organism. How does this novelty come about? Evolution builds with the tools available, and on top of what it has already built - therefore, much novelty consists in repurposing old functions in a different context. In the process, the tools themselves evolve, allowing yet more novelty to arise. Despite evolutionary novelty being the most striking observable of evolution, it is not accounted for in classical evolutionary theory. Nevertheless, mathematical and computational models that illustrate mechanisms of evolutionary innovation have been developed. In the present review, we present and compare several examples of computational evo-devo models that capture two aspects of novelty: 'between-level novelty' and 'constructive novelty.' Novelty can evolve between predefined levels of organisation to dynamically transcode biological information across these levels - as occurs during development. Constructive novelty instead generates a level of biological organisation by exploiting the lower level as an informational scaffold to open a new space of possibilities - an example being the evolution of multicellularity. We propose that the field of computational evo-devo is well-poised to reveal many more exciting mechanisms for the evolution of novelty. A broader theory of evolutionary novelty may well be attainable in the near future.
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Affiliation(s)
- Enrico Sandro Colizzi
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR, Cambridge, U.K
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Renske M A Vroomans
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR, Cambridge, U.K
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5
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Ekkers DM, Tusso S, Moreno-Gamez S, Rillo MC, Kuipers OP, van Doorn GS. Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification. Mol Biol Evol 2022; 39:msac124. [PMID: 35679426 PMCID: PMC9206417 DOI: 10.1093/molbev/msac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Mitigating trade-offs between different resource-utilization functions is key to an organism's ecological and evolutionary success. These trade-offs often reflect metabolic constraints with a complex molecular underpinning; therefore, their consequences for evolutionary processes have remained elusive. Here, we investigate how metabolic architecture induces resource utilization constraints and how these constraints, in turn, elicit evolutionary specialization and diversification. Guided by the metabolic network structure of the bacterium Lactococcus cremoris, we selected two carbon sources (fructose and galactose) with predicted co-utilization constraints. By evolving L. cremoris on either fructose, galactose or a mix of both sugars, we imposed selection favoring divergent metabolic specializations or co-utilization of both resources, respectively. Phenotypic characterization revealed the evolution of either fructose or galactose specialists in the single-sugar treatments. In the mixed sugar regime, we observed adaptive diversification: both specialists coexisted, and no generalist evolved. Divergence from the ancestral phenotype occurred at key pathway junctions in the central carbon metabolism. Fructose specialists evolved mutations in the fbp and pfk genes that appear to balance anabolic and catabolic carbon fluxes. Galactose specialists evolved increased expression of pgmA (the primary metabolic bottleneck of galactose metabolism) and silencing of ptnABCD (the main glucose transporter) and ldh (regulator/enzyme of downstream carbon metabolism). Overall, our study shows how metabolic network architecture and historical contingency serve to predict targets of selection and inform the functional interpretation of evolved mutations. The elucidation of the relationship between molecular constraints and phenotypic trade-offs contributes to an integrative understanding of evolutionary specialization and diversification.
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Affiliation(s)
- David M Ekkers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
- Science for Life Laboratories and Department of Evolutionary Biology, Norbyvägen 18D, Uppsala University, 75236 Uppsala, Sweden
| | - Stefany Moreno-Gamez
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Marina C Rillo
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - G Sander van Doorn
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Zachar I, Boza G. The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.798045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.
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Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes. Front Microbiol 2022; 12:780469. [PMID: 34987488 PMCID: PMC8721230 DOI: 10.3389/fmicb.2021.780469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/25/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.
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Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nathan Vannier
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France
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8
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Yao J, Zeng Y, Wang M, Tang YQ. Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid-Fed Anaerobic Methanogenic Chemostats. Front Microbiol 2021; 12:744834. [PMID: 34671332 PMCID: PMC8521154 DOI: 10.3389/fmicb.2021.744834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.
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Affiliation(s)
| | | | - Miaoxiao Wang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, China
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9
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Zhang IH, Mullen S, Ciccarese D, Dumit D, Martocello DE, Toyofuku M, Nomura N, Smriga S, Babbin AR. Ratio of Electron Donor to Acceptor Influences Metabolic Specialization and Denitrification Dynamics in Pseudomonas aeruginosa in a Mixed Carbon Medium. Front Microbiol 2021; 12:711073. [PMID: 34566916 PMCID: PMC8461185 DOI: 10.3389/fmicb.2021.711073] [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: 05/17/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022] Open
Abstract
Denitrifying microbes sequentially reduce nitrate (NO3 -) to nitrite (NO2 -), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx -) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx -. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Susan Mullen
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Davide Ciccarese
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Diana Dumit
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Donald E. Martocello
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Steven Smriga
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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Regueira A, Lema JM, Mauricio-Iglesias M. Microbial inefficient substrate use through the perspective of resource allocation models. Curr Opin Biotechnol 2021; 67:130-140. [PMID: 33540363 DOI: 10.1016/j.copbio.2021.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/15/2023]
Abstract
Microorganisms extract energy from substrates following strategies that may seem suboptimal at first glance. Beyond the so-called yield-rate trade-off, resource allocation models, which focus on assigning different functional roles to the limited number of enzymes that a cell can support, offer a framework to interpret the inefficient substrate use by microorganisms. We review here relevant examples of substrate conversions where a significant part of the available energy is not utilised and how resource allocation models offer a mechanistic interpretation thereof, notably for open mixed cultures. Future developments are identified, in particular, the challenge of considering metabolic flexibility towards uncertain environmental changes instead of strict fixed optimality objectives, with the final goal of increasing the prediction capabilities of resource allocation models. Finally, we highlight the relevance of resource allocation to understand and enable a promising biorefinery platform revolving around lactate, which would increase the flexibility of waste-to-chemical biorefinery schemes.
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Affiliation(s)
- Alberte Regueira
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Juan M Lema
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel Mauricio-Iglesias
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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