1
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Schmelling NM, Bross M. What is holding back cyanobacterial research and applications? A survey of the cyanobacterial research community. Nat Commun 2024; 15:6758. [PMID: 39117643 PMCID: PMC11310192 DOI: 10.1038/s41467-024-50828-6] [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: 07/12/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Cyanobacteria are a diverse group of prokaryotic organisms that have been the subject of intense basic research, resulting in a wealth of knowledge about fundamental cellular processes such as photosynthesis. However, the translation of that research towards industry-relevant applications is still limited. To understand the reasons for this contradictory situation, we conducted a quantitative survey among researchers in the cyanobacterial community, a set of individual interviews with established researchers, and a literature analysis. Our results show that the community seems to be committed to embracing cyanobacterial diversity and promoting collaboration. Additionally, participants expressed a strong desire to develop standardized protocols for research and establish larger consortia to accelerate progress. The results of the survey highlight the need for a more integrated approach to cyanobacterial research that encompasses both basic and applied aspects. Based on the survey and interview results as well as our literature analysis, we highlight areas for potential improvement, strategies to enhance cyanobacterial research, and open questions that demand further exploration. Addressing these challenges should accelerate the development of industrial applications based on cyanobacterial research.
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2
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Xu X, Liu F, Qiao W, Dong Y, Yang H, Liu F, Xu H, Qiao M. A Point Mutation in Cassette Relieves the Repression Regulation of CcpA Resulting in an Increase in the Degradation of 2,3-Butanediol in Lactococcus lactis. Microorganisms 2024; 12:773. [PMID: 38674718 PMCID: PMC11051896 DOI: 10.3390/microorganisms12040773] [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: 03/07/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In lactic acid bacteria, the global transcriptional regulator CcpA regulates carbon metabolism by repressing and activating the central carbon metabolism pathway, thus decreasing or increasing the yield of certain metabolites to maximize carbon flow. However, there are no reports on the deregulation of the inhibitory effects of CcpA on the metabolism of secondary metabolites. In this study, we identified a single-base mutant strain of Lactococcus lactis N8-2 that is capable of metabolizing 2,3-butanediol. It has been established that CcpA dissociates from the catabolite responsive element (cre) site due to a mutation, leading to the activation of derepression and expression of the 2,3-butanediol dehydrogenase gene cluster (butB and butA). Transcriptome analysis and quantitative polymerase chain reaction (Q-PCR) results showed significant upregulation of transcription of butB and butA compared to the unmutated strain. Furthermore, micro-scale thermophoresis experiments confirmed that CcpA did not bind to the mutated cre. Furthermore, in a bacterial two-plasmid fluorescent hybridization system, it was similarly confirmed that the dissociation of CcpA from cre eliminated the repressive effect of CcpA on downstream genes. Finally, we investigated the differing catalytic capacities of the 2,3-butanediol dehydrogenase gene cluster in L. lactis N8-1 and L. lactis N8-2 for 2,3-butanediol. This led to increased expression of butB and butA, which were deregulated by CcpA repression. This is the first report on the elimination of the deterrent effect of CcpA in lactic acid bacteria, which changes the direction of enzymatic catalysis and alters the direction of carbon metabolism. This provides new perspectives and strategies for metabolizing 2,3-butanediol using bacteria in synthetic biology.
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Affiliation(s)
- Xian Xu
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.X.); (Y.D.); (H.Y.); (F.L.)
| | - Fulu Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China;
| | - Wanjin Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (H.X.)
| | - Yujie Dong
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.X.); (Y.D.); (H.Y.); (F.L.)
| | - Huan Yang
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.X.); (Y.D.); (H.Y.); (F.L.)
| | - Fengming Liu
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.X.); (Y.D.); (H.Y.); (F.L.)
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (H.X.)
| | - Mingqiang Qiao
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.X.); (Y.D.); (H.Y.); (F.L.)
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (H.X.)
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3
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Douwenga S, van Olst B, Boeren S, Luo Y, Lai X, Teusink B, Vervoort J, Kleerebezem M, Bachmann H. The hierarchy of sugar catabolization in Lactococcus cremoris. Microbiol Spectr 2023; 11:e0224823. [PMID: 37888986 PMCID: PMC10715065 DOI: 10.1128/spectrum.02248-23] [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: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.
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Affiliation(s)
- Sieze Douwenga
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Berdien van Olst
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Sjef Boeren
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Yanzhang Luo
- MAGNEtic resonance research FacilitY (MAGNEFY), Wageningen University & Research, Wageningen, the Netherlands
| | - Xin Lai
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bas Teusink
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jacques Vervoort
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Microbiology Department, NIZO Food Research, Ede, the Netherlands
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4
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Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco dos Santos F, Schmelling NM. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2023; 12:1823-1835. [PMID: 37246820 PMCID: PMC10278186 DOI: 10.1021/acssynbio.3c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Indexed: 05/30/2023]
Abstract
In recent years, a plethora of new synthetic biology tools for use in cyanobacteria have been published; however, their reported characterizations often cannot be reproduced, greatly limiting the comparability of results and hindering their applicability. In this interlaboratory study, the reproducibility of a standard microbiological experiment for the cyanobacterial model organism Synechocystis sp. PCC 6803 was assessed. Participants from eight different laboratories quantified the fluorescence intensity of mVENUS as a proxy for the transcription activity of the three promoters PJ23100, PrhaBAD, and PpetE over time. In addition, growth rates were measured to compare growth conditions between laboratories. By establishing strict and standardized laboratory protocols, reflecting frequently reported methods, we aimed to identify issues with state-of-the-art procedures and assess their effect on reproducibility. Significant differences in spectrophotometer measurements across laboratories from identical samples were found, suggesting that commonly used reporting practices of optical density values need to be supplemented by cell count or biomass measurements. Further, despite standardized light intensity in the incubators, significantly different growth rates between incubators used in this study were observed, highlighting the need for additional reporting requirements of growth conditions for phototrophic organisms beyond the light intensity and CO2 supply. Despite the use of a regulatory system orthogonal to Synechocystis sp. PCC 6803, PrhaBAD, and a high level of protocol standardization, ∼32% variation in promoter activity under induced conditions was found across laboratories, suggesting that the reproducibility of other data in the field of cyanobacteria might be affected similarly.
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Affiliation(s)
- Maurice Mager
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Hugo Pineda Hernandez
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Fabian Brandenburg
- Helmholtz
Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318 Leipzig, Germany
| | - Luis López-Maury
- Instituto
de Bioquímica Vegetal y Fotosíntesis, University of Seville − CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento
de Bioquímica Vegetal y Biología Molecular, Facultad
de Biología, University of Seville, Avenida Reina Mercedes, 41012 Sevilla, Spain
| | - Alistair J. McCormick
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Dennis J. Nürnberg
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
- Dahlem
Centre of Plant Sciences, Freie Universität
Berlin, Albrecht-Thaer-Weg 6, 14195 Berlin, Germany
| | - Tim Orthwein
- Interfaculty
Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - David A. Russo
- Institute
for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743 Jena, Germany
| | - Angelo Joshua Victoria
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Xiaoran Wang
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
| | - Julie A. Z. Zedler
- Matthias
Schleiden Institute for Genetics, Bioinformatics and Molecular Botany,
Synthetic Biology of Photosynthetic Organisms, Friedrich Schiller University Jena, Dornburgerstrasse 159, 07743 Jena, Germany
| | - Filipe Branco dos Santos
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Nicolas M. Schmelling
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
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5
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Manganese Modulates Metabolic Activity and Redox Homeostasis in Translationally Blocked Lactococcus cremoris, Impacting Metabolic Persistence, Cell Culturability, and Flavor Formation. Microbiol Spectr 2022; 10:e0270821. [PMID: 35638825 PMCID: PMC9241929 DOI: 10.1128/spectrum.02708-21] [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] [Indexed: 11/20/2022] Open
Abstract
Manganese (Mn) is an essential trace element that is supplemented in microbial media with varying benefits across species and growth conditions. We found that growth of Lactococcus cremoris was unaffected by manganese omission from the growth medium. The main proteome adaptation to manganese omission involved increased manganese transporter production (up to 2,000-fold), while the remaining 10 significant proteome changes were between 1.4- and 4-fold. Further investigation in translationally blocked (TB), nongrowing cells showed that Mn supplementation (20 μM) led to approximately 1.5 X faster acidification compared with Mn-free conditions. However, this faster acidification stagnated within 24 h, likely due to draining of intracellular NADH that coincides with substantial loss of culturability. Conversely, without manganese, nongrowing cells persisted to acidify for weeks, albeit at a reduced rate, but maintaining redox balance and culturability. Strikingly, despite being unculturable, α-keto acid-derived aldehydes continued to accumulate in cells incubated in the presence of manganese, whereas without manganese cells predominantly formed the corresponding alcohols. This is most likely reflecting NADH availability for the alcohol dehydrogenase-catalyzed conversion. Overall, manganese influences the lactococcal acidification rate, and flavor formation capacity in a redox dependent manner. These are important industrial traits especially during cheese ripening, where cells are in a non-growing, often unculturable state. IMPORTANCE In nature as well as in various biotechnology applications, microorganisms are often in a nongrowing state and their metabolic persistence determines cell survival and functionality. Industrial examples are dairy fermentations where bacteria remain active during the ripening phases that can take up to months and even years. Here we investigated environmental factors that can influence lactococcal metabolic persistence throughout such prolonged periods. We found that in the absence of manganese, acidification of nongrowing cells remained active for weeks while in the presence of manganese it stopped within 1 day. The latter coincided with the accumulation of amino acid derived volatile metabolites. Based on metabolic conversions, proteome analysis, and a reporter assay, we demonstrated that the manganese elicited effects were NADH dependent. Overall the results show the effect of environmental modulation on prolonged cell-based catalysis, which is highly relevant to non-growing cells in nature and biotechnological applications.
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6
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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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7
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Douwenga S, van Tatenhove-Pel RJ, Zwering E, Bachmann H. Stationary Lactococcus cremoris: Energetic State, Protein Synthesis Without Nitrogen and Their Effect on Survival. Front Microbiol 2021; 12:794316. [PMID: 34975819 PMCID: PMC8719527 DOI: 10.3389/fmicb.2021.794316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
During storage and ripening of fermented foods, Lactococcus cremoris is predominantly in a non-growing state. L. cremoris can become stationary due to starvation or acidification, and its metabolism in these non-growing states affects the fermented product. Available studies on the response of L. cremoris to acid and starvation stress are based on population level data. We here characterized the energetic state and the protein synthesis capacity of stationary L. cremoris cultures at the single cell level. We show that glucose starved stationary cells are energy-depleted, while acid-induced stationary cells are energized and can maintain a pH gradient over their membrane. In the absence of glucose and arginine, a small pH gradient can still be maintained. Subpopulations of stationary cells can synthesize protein without a nitrogen source, and the subpopulation size decreases with increasing stationary phase length. Protein synthesis capacity during starvation only benefits culturability after 6 days. These results highlight significant differences between glucose starved stationary and acid-induced stationary cells. Furthermore, they show that the physiology of stationary phase L. cremoris cells is multi-facetted and heterogeneous, and the presence of an energy source during stationary phase impacts the cells capacity to adapt to their environment.
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Affiliation(s)
- Sieze Douwenga
- TiFN, Wageningen, Netherlands
- Systems Biology Lab, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Rinke J. van Tatenhove-Pel
- Systems Biology Lab, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Emile Zwering
- Systems Biology Lab, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Herwig Bachmann
- TiFN, Wageningen, Netherlands
- Systems Biology Lab, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- NIZO, Ede, Netherlands
- *Correspondence: Herwig Bachmann,
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8
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van Tatenhove-Pel RJ, de Groot DH, Bisseswar AS, Teusink B, Bachmann H. Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth. THE ISME JOURNAL 2021; 15:3050-3061. [PMID: 33953364 PMCID: PMC8443577 DOI: 10.1038/s41396-021-00986-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/29/2021] [Accepted: 04/09/2021] [Indexed: 02/01/2023]
Abstract
As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. However, in many natural systems cells can also grow to low cell concentrations in the absence of these exchanged molecules, thus showing "cooperation-independent background growth". We here serially propagated a synthetic cross-feeding consortium of lactococci in the droplets of a water-in-oil emulsion, essentially mimicking group selection with varying founder population sizes. The results show that when the growth of cheaters completely depends on cooperators, cooperators outcompete cheaters. However, cheaters outcompete cooperators when they can independently grow to only ten percent of the consortium carrying capacity. This result is the consequence of a probabilistic effect, as low founder population sizes in droplets decrease the frequency of cooperator co-localization. Cooperator-enrichment can be recovered by increasing the founder population size in droplets to intermediate values. Together with mathematical modelling our results suggest that co-localization probabilities in a spatially structured environment leave a small window of opportunity for the evolution of cooperation between organisms that do not benefit from their cooperative trait when in isolation or form multispecies aggregates.
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Affiliation(s)
- Rinke J. van Tatenhove-Pel
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands ,grid.5292.c0000 0001 2097 4740Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands
| | - Daan H. de Groot
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands
| | - Anjani S. Bisseswar
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands
| | - Bas Teusink
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands
| | - Herwig Bachmann
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands ,grid.419921.60000 0004 0588 7915NIZO Food Research, Kernhemseweg 2, Ede, The Netherlands
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9
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Growth, dormancy and lysis: the complex relation of starter culture physiology and cheese flavour formation. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Chen Y, van Pelt‐KleinJan E, van Olst B, Douwenga S, Boeren S, Bachmann H, Molenaar D, Nielsen J, Teusink B. Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments. Mol Syst Biol 2021; 17:e10093. [PMID: 33821549 PMCID: PMC8022198 DOI: 10.15252/msb.202010093] [Citation(s) in RCA: 21] [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: 11/03/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Cells adapt to different conditions via gene expression that tunes metabolism for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade-offs. Resource allocation under proteome constraints has explained regulatory strategies in bacteria. It is unclear, however, to what extent these constraints can predict evolutionary changes, especially for microorganisms that evolved under nutrient-rich conditions, i.e., multiple available nitrogen sources, such as Lactococcus lactis. Here, we present a proteome-constrained genome-scale metabolic model of L. lactis (pcLactis) to interpret growth on multiple nutrients. Through integration of proteomics and flux data, in glucose-limited chemostats, the model predicted glucose and arginine uptake as dominant constraints at low growth rates. Indeed, glucose and arginine catabolism were found upregulated in evolved mutants. At high growth rates, pcLactis correctly predicted the observed shutdown of arginine catabolism because limited proteome availability favored lactate for ATP production. Thus, our model-based analysis is able to identify and explain the proteome constraints that limit growth rate in nutrient-rich environments and thus form targets of fitness improvement.
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Affiliation(s)
- Yu Chen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for BiosustainabilityChalmers University of TechnologyGothenburgSweden
| | - Eunice van Pelt‐KleinJan
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Berdien van Olst
- TiFNWageningenthe Netherlands
- Host‐Microbe InteractomicsWageningen University & ResearchWageningenThe Netherlands
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Sieze Douwenga
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sjef Boeren
- TiFNWageningenthe Netherlands
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Herwig Bachmann
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
- NIZO Food ResearchEdeThe Netherlands
| | - Douwe Molenaar
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for BiosustainabilityChalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
- BioInnovation InstituteCopenhagen NDenmark
| | - Bas Teusink
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
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11
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Bruggeman FJ, Planqué R, Molenaar D, Teusink B. Searching for principles of microbial physiology. FEMS Microbiol Rev 2021; 44:821-844. [PMID: 33099619 PMCID: PMC7685786 DOI: 10.1093/femsre/fuaa034] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/02/2020] [Indexed: 12/27/2022] Open
Abstract
Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.
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Affiliation(s)
- Frank J Bruggeman
- Systems Biology Lab, AIMMS, De Boelelaan 1108, 1081 HZ, VU University, Amsterdam, The Netherlands
| | - Robert Planqué
- Department of Mathematics, De Boelelaan 1111, 1081 HV, VU University, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Systems Biology Lab, AIMMS, De Boelelaan 1108, 1081 HZ, VU University, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, AIMMS, De Boelelaan 1108, 1081 HZ, VU University, Amsterdam, The Netherlands
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12
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Kleerebezem M, Bachmann H, van Pelt-KleinJan E, Douwenga S, Smid EJ, Teusink B, van Mastrigt O. Lifestyle, metabolism and environmental adaptation in Lactococcus lactis. FEMS Microbiol Rev 2021; 44:804-820. [PMID: 32990728 DOI: 10.1093/femsre/fuaa033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.
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Affiliation(s)
- Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands
| | - Eunice van Pelt-KleinJan
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Sieze Douwenga
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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13
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Nugroho ADW, Kleerebezem M, Bachmann H. A Novel Method for Long-Term Analysis of Lactic Acid and Ammonium Production in Non-growing Lactococcus lactis Reveals Pre-culture and Strain Dependence. Front Bioeng Biotechnol 2020; 8:580090. [PMID: 33163481 PMCID: PMC7580867 DOI: 10.3389/fbioe.2020.580090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/15/2020] [Indexed: 01/25/2023] Open
Abstract
In various (industrial) conditions, cells are in a non-growing but metabolically active state in which de novo protein synthesis capacity is limited. The production of a metabolite by such non-growing cells is dependent on the cellular condition and enzyme activities, such as the amount, stability, and degradation of the enzyme(s). For industrial fermentations in which the metabolites of interest are mainly formed after cells enter the stationary phase, the investigation of prolonged metabolite production is of great importance. However, current batch model systems do not allow prolonged measurements due to metabolite accumulation driving product-inhibition. Here we developed a protocol that allows high-throughput metabolic measurements to be followed in real-time over extended periods (weeks). As a validation model, sugar utilization and arginine consumption by a low density of translationally blocked Lactococcus lactis was designed in a defined medium. In this system L. lactis MG1363 was compared with its derivative HB60, a strain described to achieve higher metabolic yield through a shift toward heterofermentative metabolism. The results showed that in a non-growing state HB60 is able to utilize more arginine than MG1363, and for both strains the decay of the measured activities were dependent on pre-culture conditions. During the first 5 days of monitoring a ∼25-fold decrease in acidification rate was found for strain HB60 as compared to a ∼20-fold decrease for strain MG1363. Such measurements are relevant for the understanding of microbial metabolism and for optimizing applications in which cells are frequently exposed to long-term suboptimal conditions, such as microbial cell factories, fermentation ripening, and storage survival.
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Affiliation(s)
- Avis Dwi Wahyu Nugroho
- TiFN, Wageningen, Netherlands.,Health Department, NIZO Food Research, Ede, Netherlands.,Laboratory of Host-Microbe Interactomics, Wageningen University and Research Centers, Wageningen, Netherlands
| | - Michiel Kleerebezem
- TiFN, Wageningen, Netherlands.,Laboratory of Host-Microbe Interactomics, Wageningen University and Research Centers, Wageningen, Netherlands
| | - Herwig Bachmann
- TiFN, Wageningen, Netherlands.,Health Department, NIZO Food Research, Ede, Netherlands.,Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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14
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Ekkers DM, Branco dos Santos F, Mallon CA, Bruggeman F, van Doorn GS. The omnistat: A flexible continuous-culture system for prolonged experimental evolution. Methods Ecol Evol 2020; 11:932-942. [PMID: 32999708 PMCID: PMC7508058 DOI: 10.1111/2041-210x.13403] [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: 06/13/2019] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
Microbial evolution experiments provide a powerful tool to unravel the molecular basis of adaptive evolution but their outcomes can be difficult to interpret, unless the selective forces that are applied during the experiment are carefully controlled. In this respect, experimental evolution in continuous cultures provides advantages over commonly used sequential batch-culture protocols because continuous cultures allow for more accurate control over the induced selective environment. However, commercial continuous-culture systems are large and expensive, while available DIY continuous-culture systems are not versatile enough to allow for multiple sensors and rigorous stirring.We present a modular continuous-culture system that adopts the commonly used GL45 glass laboratory bottle as a bioreactor vessel. Our design offers three advantages: first, it is equipped with a large head plate, fitting two sensors and seven input/output ports, enabling the customization of the system for many running modes (chemostat, auxostat, etc.). Second, the bioreactor is small (25-250 ml), which makes it feasible to run many replicates in parallel. Third, bioreactor modules can be coupled by uni- or bi-directional flows to induce spatiotemporal variation in selection. These features result in a particularly flexible culturing platform that facilitates the investigation of a broad range of evolutionary and ecological questions.To illustrate the versatility of our culturing system, we outline two evolution experiments that impose a temporally or spatially variable regime of selection. The first experiment illustrates how controlled temporal variation in resource availability can be utilized to select for anticipatory switching. The second experiment illustrates a spatially structured morbidostat setup that is designed to probe epistatic interactions between adaptive mutations. Furthermore, we demonstrate how sensor data can be used to stabilize selection pressures or track evolutionary adaptation.Evolution experiments in which populations are exposed to controlled spatiotemporal variation, are essential to gain insight into the process of adaptation and the mechanisms that constrain evolution. Continuous-culture systems, like the one presented here, offer control over key environmental parameters and establish a well-defined regime of selection. As such, they create the opportunity to expose evolutionary constraints in the form of phenotypic trade-offs, contributing to a mechanistic understanding of adaptive evolution.
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Affiliation(s)
- David M. Ekkers
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology GroupFaculty of ScienceSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems BiologyVU UniversityAmsterdamThe Netherlands
| | - Cyrus A. Mallon
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Frank Bruggeman
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems BiologyVU UniversityAmsterdamThe Netherlands
| | - G. Sander van Doorn
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
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15
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Tarazanova M, Huppertz T, Starrenburg M, Todt T, van Hijum S, Kok J, Bachmann H. Transcriptional response of Lactococcus lactis during bacterial emulsification. PLoS One 2019; 14:e0220048. [PMID: 31344087 PMCID: PMC6657864 DOI: 10.1371/journal.pone.0220048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/08/2019] [Indexed: 12/25/2022] Open
Abstract
Microbial surface properties are important for interactions with the environment in which cells reside. Surface properties of lactic acid bacteria significantly vary and some strains can form strong emulsions when mixed with a hydrocarbon. Lactococcus lactis NCDO712 forms oil-in-water emulsions upon mixing of a cell suspension with petroleum. In the emulsion the bacteria locate at the oil-water interphase which is consistent with Pickering stabilization. Cells of strain NCDO712 mixed with sunflower seed oil did not stabilize the oil droplets. This study shows that the addition of either ethanol or ammonium sulfate led to cell aggregation, which subsequently allowed stabilizing oil-in-water emulsions. From this, we conclude that bacterial cell aggregation is important for emulsion droplet stabilization. To determine how bacterial emulsification influences the microbial transcriptome RNAseq analysis was performed on lactococci taken from the oil-water interphase. In comparison to cells in suspension 72 genes were significantly differentially expressed with a more than 4-fold difference. The majority of these genes encode proteins involved in transport processes and the metabolism of amino acids, carbohydrates and ions. Especially the proportion of genes belonging to the CodY regulon was high. Our results also point out that in a complex environment such as food fermentations a heterogeneous response of microbes might be caused by microbe-matrix interactions. In addition, microdroplet technologies are increasingly used in research. The understanding of interactions between bacterial cells and oil-water interphases is of importance for conducting and interpreting such experiments.
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Affiliation(s)
- Mariya Tarazanova
- TI Food and Nutrition, AN Wageningen, The Netherlands
- NIZO, Ede BA, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Thom Huppertz
- TI Food and Nutrition, AN Wageningen, The Netherlands
- NIZO, Ede BA, The Netherlands
| | - Marjo Starrenburg
- TI Food and Nutrition, AN Wageningen, The Netherlands
- NIZO, Ede BA, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Tilman Todt
- Radboud University Medical Centre CMBI, Geert Grooteplein Nijmegen, The Netherlands
- HAN, University of Applied Sciences, PGL Nijmegen, The Netherlands
| | - Sacha van Hijum
- TI Food and Nutrition, AN Wageningen, The Netherlands
- NIZO, Ede BA, The Netherlands
- Radboud University Medical Centre CMBI, Geert Grooteplein Nijmegen, The Netherlands
| | - Jan Kok
- TI Food and Nutrition, AN Wageningen, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, AN Wageningen, The Netherlands
- NIZO, Ede BA, The Netherlands
- * E-mail:
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