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Moreno-Paz S, van der Hoek R, Eliana E, Zwartjens P, Gosiewska S, Martins dos Santos VAP, Schmitz J, Suarez-Diez M. Machine Learning-Guided Optimization of p-Coumaric Acid Production in Yeast. ACS Synth Biol 2024; 13:1312-1322. [PMID: 38545878 PMCID: PMC11036487 DOI: 10.1021/acssynbio.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024]
Abstract
Industrial biotechnology uses Design-Build-Test-Learn (DBTL) cycles to accelerate the development of microbial cell factories, required for the transition to a biobased economy. To use them effectively, appropriate connections between the phases of the cycle are crucial. Using p-coumaric acid (pCA) production in Saccharomyces cerevisiae as a case study, we propose the use of one-pot library generation, random screening, targeted sequencing, and machine learning (ML) as links during DBTL cycles. We showed that the robustness and flexibility of the ML models strongly enable pathway optimization and propose feature importance and Shapley additive explanation values as a guide to expand the design space of original libraries. This approach allowed a 68% increased production of pCA within two DBTL cycles, leading to a 0.52 g/L titer and a 0.03 g/g yield on glucose.
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Affiliation(s)
- Sara Moreno-Paz
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, 6708 WE Wageningen, The Netherlands
| | - Rianne van der Hoek
- Department
of Science and Research, dsm-firmenich,
Science & Research, 2600 MA Delft, The
Netherlands
| | - Elif Eliana
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, 6708 WE Wageningen, The Netherlands
| | - Priscilla Zwartjens
- Department
of Science and Research, dsm-firmenich,
Science & Research, 2600 MA Delft, The
Netherlands
| | - Silvia Gosiewska
- Department
of Science and Research, dsm-firmenich,
Science & Research, 2600 MA Delft, The
Netherlands
| | | | - Joep Schmitz
- Department
of Science and Research, dsm-firmenich,
Science & Research, 2600 MA Delft, The
Netherlands
| | - Maria Suarez-Diez
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, 6708 WE Wageningen, The Netherlands
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2
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Moreno-Paz S, van der Hoek R, Eliana E, Martins Dos Santos VAP, Schmitz J, Suarez-Diez M. Combinatorial optimization of pathway, process and media for the production of p-coumaric acid by Saccharomyces cerevisiae. Microb Biotechnol 2024; 17:e14424. [PMID: 38528768 DOI: 10.1111/1751-7915.14424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 03/27/2024] Open
Abstract
Microbial cell factories are instrumental in transitioning towards a sustainable bio-based economy, offering alternatives to conventional chemical processes. However, fulfilling their potential requires simultaneous screening for optimal media composition, process and genetic factors, acknowledging the complex interplay between the organism's genotype and its environment. This study employs statistical design of experiments to systematically explore these relationships and optimize the production of p-coumaric acid (pCA) in Saccharomyces cerevisiae. Two rounds of fractional factorial designs were used to identify factors with a significant effect on pCA production, which resulted in a 168-fold variation in pCA titre. Moreover, a significant interaction between the culture temperature and expression of ARO4 highlighted the importance of simultaneous process and strain optimization. The presented approach leverages the strengths of experimental design and statistical analysis and could be systematically applied during strain and bioprocess design efforts to unlock the full potential of microbial cell factories.
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Affiliation(s)
- Sara Moreno-Paz
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Rianne van der Hoek
- Department of Science and Research-dsm-firmenich, Science & Research, Delft, The Netherlands
| | - Elif Eliana
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Joep Schmitz
- Department of Science and Research-dsm-firmenich, Science & Research, Delft, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
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Scott WT, Benito-Vaquerizo S, Zimmermann J, Bajić D, Heinken A, Suarez-Diez M, Schaap PJ. A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. PLoS Comput Biol 2023; 19:e1011363. [PMID: 37578975 PMCID: PMC10449394 DOI: 10.1371/journal.pcbi.1011363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
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Affiliation(s)
- William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
| | - Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany
| | - Djordje Bajić
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Almut Heinken
- Inserm U1256 Laboratoire nGERE, Université de Lorraine, Nancy, France
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
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4
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Benito-Vaquerizo S, Nouse N, Schaap PJ, Hugenholtz J, Brul S, López-Contreras AM, Martins dos Santos VAP, Suarez-Diez M. Model-driven approach for the production of butyrate from CO 2/H 2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Front Microbiol 2022; 13:1064013. [PMID: 36620068 PMCID: PMC9815533 DOI: 10.3389/fmicb.2022.1064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Niels Nouse
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,UNLOCK Large Scale Infrastructure for Microbial Communities, Wageningen University and Research and Delft University of Technology, Wageningen, Netherlands
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Ana M. López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, Netherlands
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Maria Suarez-Diez ✉
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5
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González-Plaza JJ, Furlan C, Rijavec T, Lapanje A, Barros R, Tamayo-Ramos JA, Suarez-Diez M. Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels. Front Microbiol 2022; 13:1006946. [PMID: 36519168 PMCID: PMC9744117 DOI: 10.3389/fmicb.2022.1006946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 08/31/2023] Open
Abstract
The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.
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Affiliation(s)
- Juan José González-Plaza
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Rocío Barros
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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6
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Budimir I, Giampieri E, Saccenti E, Suarez-Diez M, Tarozzi M, Dall'Olio D, Merlotti A, Curti N, Remondini D, Castellani G, Sala C. Intraspecies characterization of bacteria via evolutionary modeling of protein domains. Sci Rep 2022; 12:16595. [PMID: 36198716 PMCID: PMC9534902 DOI: 10.1038/s41598-022-21036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.
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Affiliation(s)
- Iva Budimir
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Martina Tarozzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniele Dall'Olio
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Alessandra Merlotti
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
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7
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Masłowska-Górnicz A, van den Bosch MRM, Saccenti E, Suarez-Diez M. A large-scale analysis of codon usage bias in 4868 bacterial genomes shows association of codon adaptation index with GC content, protein functional domains and bacterial phenotypes. Biochim Biophys Acta Gene Regul Mech 2022; 1865:194826. [PMID: 35605953 DOI: 10.1016/j.bbagrm.2022.194826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Multiple synonymous codons code for the same amino acid, resulting in the degeneracy of the genetic code and in the preferred used of some codons called codon bias usage (CBU). We performed a large-scale analysis of codon usage bias analysing the distribution of the codon adaptation index (CAI) and the codon relative adaptiveness index (RA) in 4868 bacterial genomes. We found that CAI values differ significantly between protein functional domains and part of the protein outside domains and show how CAI, GC content and preferred usage of polymerase III alpha subunits are related. Additionally, we give evidence of the association between CAI and bacterial phenotypes.
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Affiliation(s)
- Anna Masłowska-Górnicz
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Melanie R M van den Bosch
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
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8
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Benito-Vaquerizo S, Parera Olm I, de Vroet T, Schaap PJ, Sousa DZ, Martins Dos Santos VAP, Suarez-Diez M. Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. Microb Cell Fact 2022; 21:116. [PMID: 35710409 PMCID: PMC9205015 DOI: 10.1186/s12934-022-01841-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate. RESULTS Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium. CONCLUSIONS The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Thijs de Vroet
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Vening Meinesz building C, Princetonlaan 6, Utrecht, 3584 CB, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Bioprocess Engineering, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.
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9
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Zakhartsev M, Rotnes F, Gulla M, Øyås O, van Dam JCJ, Suarez-Diez M, Grammes F, Hafþórsson RA, van Helvoirt W, Koehorst JJ, Schaap PJ, Jin Y, Mydland LT, Gjuvsland AB, Sandve SR, Martins dos Santos VAP, Vik JO. SALARECON connects the Atlantic salmon genome to growth and feed efficiency. PLoS Comput Biol 2022; 18:e1010194. [PMID: 35687595 PMCID: PMC9223387 DOI: 10.1371/journal.pcbi.1010194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 06/23/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon. We present SALARECON, a model focusing on energy, amino acid, and nucleotide metabolism that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and captures expected metabolic (in)capabilities. We show that it can explain observed hypoxic growth in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted limiting amino acids and feed efficiencies agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture such as development of sustainable feeds. Atlantic salmon aquaculture generates billions of euros annually, but faces challenges of sustainability. Salmon are carnivores by nature, and fish oil and fish meal have become scarce resources in fish feed production. Novel, sustainable feedstuffs are being trialed hand in hand with studies of the genetics of growth and feed efficiency. This calls for a mathematical-biological framework to integrate data with understanding of the effects of novel feeds on salmon physiology and its interplay with genetics. We have developed the SALARECON model of the core salmon metabolic reaction network, linking its genome to metabolic fluxes and growth. Computational analyses show good agreement with observed growth, amino acid limitations, and feed efficiencies, illustrating the potential for in silico studies of potential feed mixtures. In particular, in silico screening of possible diets will enable more efficient animal experiments with improved knowledge gain. We have adopted best practices for test-driven development, virtual experiments to assay metabolic capabilities, revision control, and FAIR data and model management. This facilitates fast, collaborative, reliable development of the model for future applications in sustainable production biology.
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Affiliation(s)
- Maksim Zakhartsev
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Filip Rotnes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Marie Gulla
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ove Øyås
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jesse C. J. van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Fabian Grammes
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | | | - Wout van Helvoirt
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Yang Jin
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Liv Torunn Mydland
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Arne B. Gjuvsland
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Simen R. Sandve
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | | | - Jon Olav Vik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
- * E-mail:
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10
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Ferrer L, Mindt M, Suarez-Diez M, Jilg T, Zagorščak M, Lee JH, Gruden K, Wendisch VF, Cankar K. Fermentative Indole Production via Bacterial Tryptophan Synthase Alpha Subunit and Plant Indole-3-Glycerol Phosphate Lyase Enzymes. J Agric Food Chem 2022; 70:5634-5645. [PMID: 35500281 PMCID: PMC9100643 DOI: 10.1021/acs.jafc.2c01042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol phosphate (IGP) by plant indole-3-glycerol phosphate lyases (IGLs). While it is widely accepted that the tryptophan synthase α-subunit (TSA) has intrinsically low IGL activity in the absence of the tryptophan synthase β-subunit, in this study, we show that Corynebacterium glutamicum TSA functions as a bona fide IGL and can support fermentative indole production in strains providing IGP. By bioprospecting additional bacterial TSAs and plant IGLs that function as bona fide IGLs were identified. Capturing indole in an overlay enabled indole production to titers of about 0.7 g L-1 in fermentations using C. glutamicum strains expressing either the endogenous TSA gene or the IGL gene from wheat.
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Affiliation(s)
- Lenny Ferrer
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Melanie Mindt
- Wageningen
Plant Research, Wageningen University &
Research, 6708PB Wageningen, The Netherlands
- Axxence
Aromatic GmbH, 46446 Emmerich am Rhein, Germany
| | - Maria Suarez-Diez
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, 6708WE Wageningen, The Netherlands
| | - Tatjana Jilg
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Maja Zagorščak
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Jin-Ho Lee
- Department
of Food Science & Biotechnology, Kyungsung
University, 608-736 Busan, Republic of Korea
| | - Kristina Gruden
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Volker F. Wendisch
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Katarina Cankar
- Wageningen
Plant Research, Wageningen University &
Research, 6708PB Wageningen, The Netherlands
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11
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Mindt M, Beyraghdar Kashkooli A, Suarez-Diez M, Ferrer L, Jilg T, Bosch D, Martins Dos Santos V, Wendisch VF, Cankar K. Production of indole by Corynebacterium glutamicum microbial cell factories for flavor and fragrance applications. Microb Cell Fact 2022; 21:45. [PMID: 35331232 PMCID: PMC8944080 DOI: 10.1186/s12934-022-01771-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/01/2022] [Indexed: 02/07/2023] Open
Abstract
Background The nitrogen containing aromatic compound indole is known for its floral odor typical of jasmine blossoms. Due to its characteristic scent, it is frequently used in dairy products, tea drinks and fine fragrances. The demand for natural indole by the flavor and fragrance industry is high, yet, its abundance in essential oils isolated from plants such as jasmine and narcissus is low. Thus, there is a strong demand for a sustainable method to produce food-grade indole. Results Here, we established the biotechnological production of indole upon l-tryptophan supplementation in the bacterial host Corynebacterium glutamicum. Heterologous expression of the tryptophanase gene from E. coli enabled the conversion of supplemented l-tryptophan to indole. Engineering of the substrate import by co-expression of the native aromatic amino acid permease gene aroP increased whole-cell biotransformation of l-tryptophan to indole by two-fold. Indole production to 0.2 g L−1 was achieved upon feeding of 1 g L−1l-tryptophan in a bioreactor cultivation, while neither accumulation of side-products nor loss of indole were observed. To establish an efficient and robust production process, new tryptophanases were recruited by mining of bacterial sequence databases. This search retrieved more than 400 candidates and, upon screening of tryptophanase activity, nine new enzymes were identified as most promising. The highest production of indole in vivo in C. glutamicum was achieved based on the tryptophanase from Providencia rettgeri. Evaluation of several biological aspects identified the product toxicity as major bottleneck of this conversion. In situ product recovery was applied to sequester indole in a food-grade organic phase during the fermentation to avoid inhibition due to product accumulation. This process enabled complete conversion of l-tryptophan and an indole product titer of 5.7 g L−1 was reached. Indole partitioned to the organic phase which contained 28 g L−1 indole while no other products were observed indicating high indole purity. Conclusions The bioconversion production process established in this study provides an attractive route for sustainable indole production from tryptophan in C. glutamicum. Industrially relevant indole titers were achieved within 24 h and indole was concentrated in the organic layer as a pure product after the fermentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01771-y.
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Affiliation(s)
- Melanie Mindt
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands.,Axxence Aromatic GmbH, Emmerich am Rhein, Germany
| | - Arman Beyraghdar Kashkooli
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Lenny Ferrer
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Tatjana Jilg
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Dirk Bosch
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Vitor Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.,Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Katarina Cankar
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands.
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12
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Moreno-Paz S, Schmitz J, Martins Dos Santos VAP, Suarez-Diez M. Enzyme-constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed-batch bioreactors. Microb Biotechnol 2022; 15:1434-1445. [PMID: 35048533 PMCID: PMC9049605 DOI: 10.1111/1751-7915.13995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/23/2021] [Accepted: 12/05/2021] [Indexed: 11/29/2022] Open
Abstract
Genome‐scale, constraint‐based models (GEM) and their derivatives are commonly used to model and gain insights into microbial metabolism. Often, however, their accuracy and predictive power are limited and enable only approximate designs. To improve their usefulness for strain and bioprocess design, we studied here their capacity to accurately predict metabolic changes in response to operational conditions in a bioreactor, as well as intracellular, active reactions. We used flux balance analysis (FBA) and dynamic FBA (dFBA) to predict growth dynamics of the model organism Saccharomyces cerevisiae under different industrially relevant conditions. We compared simulations with the latest developed GEM for this organism (Yeast8) and its enzyme‐constrained version (ecYeast8) herein described with experimental data and found that ecYeast8 outperforms Yeast8 in all the simulations. EcYeast8 was able to predict well‐known traits of yeast metabolism including the onset of the Crabtree effect, the order of substrate consumption during mixed carbon cultivation and production of a target metabolite. We showed how the combination of ecGEM and dFBA links reactor operation and genetic modifications to flux predictions, enabling the prediction of yields and productivities of different strains and (dynamic) production processes. Additionally, we present flux sampling as a tool to analyse flux predictions of ecGEM, of major importance for strain design applications. We showed that constraining protein availability substantially improves accuracy of the description of the metabolic state of the cell under dynamic conditions. This therefore enables more realistic and faithful designs of industrially relevant cell‐based processes and, thus, the usefulness of such models.
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Affiliation(s)
- Sara Moreno-Paz
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Joep Schmitz
- DSM Biotechnology Center, DSM, Delft, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.,Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands.,Lifeglimmer GmbH, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
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13
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Mollaei M, Suarez-Diez M, Sedano-Nunez VT, Boeren S, Stams AJM, Plugge CM. Proteomic Analysis of a Syntrophic Coculture of Syntrophobacter fumaroxidans MPOB T and Geobacter sulfurreducens PCA T. Front Microbiol 2021; 12:708911. [PMID: 34950111 PMCID: PMC8691401 DOI: 10.3389/fmicb.2021.708911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
We established a syntrophic coculture of Syntrophobacter fumaroxidans MPOBT (SF) and Geobacter sulfurreducens PCAT (GS) growing on propionate and Fe(III). Neither of the bacteria was capable of growth on propionate and Fe(III) in pure culture. Propionate degradation by SF provides acetate, hydrogen, and/or formate that can be used as electron donors by GS with Fe(III) citrate as electron acceptor. Proteomic analyses of the SF-GS coculture revealed propionate conversion via the methylmalonyl-CoA (MMC) pathway by SF. The possibility of interspecies electron transfer (IET) via direct (DIET) and/or hydrogen/formate transfer (HFIT) was investigated by comparing the differential abundance of associated proteins in SF-GS coculture against (i) SF coculture with Methanospirillum hungatei (SF-MH), which relies on HFIT, (ii) GS pure culture growing on acetate, formate, hydrogen as propionate products, and Fe(III). We noted some evidence for DIET in the SF-GS coculture, i.e., GS in the coculture showed significantly lower abundance of uptake hydrogenase (43-fold) and formate dehydrogenase (45-fold) and significantly higher abundance of proteins related to acetate metabolism (i.e., GltA; 62-fold) compared to GS pure culture. Moreover, SF in the SF-GS coculture showed significantly lower abundance of IET-related formate dehydrogenases, Fdh3 (51-fold) and Fdh5 (29-fold), and the rate of propionate conversion in SF-GS was 8-fold lower than in the SF-MH coculture. In contrast, compared to GS pure culture, we found lower abundance of pilus-associated cytochrome OmcS (2-fold) and piliA (5-fold) in the SF-GS coculture that is suggested to be necessary for DIET. Furthermore, neither visible aggregates formed in the SF-GS coculture, nor the pili-E of SF (suggested as e-pili) were detected. These findings suggest that the IET mechanism is complex in the SF-GS coculture and can be mediated by several mechanisms rather than one discrete pathway. Our study can be further useful in understanding syntrophic propionate degradation in bioelectrochemical and anaerobic digestion systems.
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Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M. Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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14
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Sinha N, van Schothorst EM, Hooiveld GJEJ, Keijer J, Martins Dos Santos VAP, Suarez-Diez M. Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism. BMC Bioinformatics 2021; 22:574. [PMID: 34839828 PMCID: PMC8628452 DOI: 10.1186/s12859-021-04488-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 11/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher flux values. RESULTS Here, we extended E-Flux and systematically evaluated the impact of an assumed proportionality constant on model predictions. We used data from published experiments with Escherichia coli and Saccharomyces cerevisiae and we compared the predictions of the algorithm to measured extracellular and intracellular fluxes. CONCLUSION We showed that detailed modelling using a proportionality constant can greatly impact the outcome of the analysis. This increases accuracy and allows for extraction of better physiological information.
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Affiliation(s)
- Neeraj Sinha
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Human and Animal Physiology, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Evert M van Schothorst
- Human and Animal Physiology, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,LifeGlimmer GmbH., Markelstrasse 38, 12163, Berlin, Germany.,Bioprocess Engineering Group, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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15
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Martel Martín S, Barros R, Domi B, Rumbo C, Poddighe M, Aparicio S, Suarez-Diez M, Tamayo-Ramos JA. Low Toxicological Impact of Commercial Pristine Multi-Walled Carbon Nanotubes on the Yeast Saccharomyces cerevisiae. Nanomaterials (Basel) 2021; 11:nano11092272. [PMID: 34578588 PMCID: PMC8471963 DOI: 10.3390/nano11092272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 11/16/2022]
Abstract
Carbon nanotubes (CNTs) have attracted the attention of academy and industry due to their potential applications, being currently produced and commercialized at a mass scale, but their possible impact on different biological systems remains unclear. In the present work, an assessment to understand the toxicity of commercial pristine multi-walled carbon nanotubes (MWCNTs) on the unicellular fungal model Saccharomyces cerevisiae is presented. Firstly, the nanomaterial was physico-chemically characterized, to obtain insights concerning its morphological features and elemental composition. Afterwards, a toxicology assessment was carried out, where it could be observed that cell proliferation was negatively affected only in the presence of 800 mg L-1 for 24 h, while oxidative stress was induced at a lower concentration (160 mg L-1) after a short exposure period (2 h). Finally, to identify possible toxicity pathways induced by the selected MWCNTs, the transcriptome of S. cerevisiae exposed to 160 and 800 mg L-1, for two hours, was studied. In contrast to a previous study, reporting massive transcriptional changes when yeast cells were exposed to graphene nanoplatelets in the same exposure conditions, only a small number of genes (130) showed significant transcriptional changes in the presence of MWCNTs, in the higher concentration tested (800 mg L-1), and most of them were found to be downregulated, indicating a limited biological response of the yeast cells exposed to the selected pristine commercial CNTs.
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Affiliation(s)
- Sonia Martel Martín
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain; (S.M.M.); (R.B.); (B.D.); (C.R.); (S.A.)
| | - Rocío Barros
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain; (S.M.M.); (R.B.); (B.D.); (C.R.); (S.A.)
| | - Brixhilda Domi
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain; (S.M.M.); (R.B.); (B.D.); (C.R.); (S.A.)
| | - Carlos Rumbo
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain; (S.M.M.); (R.B.); (B.D.); (C.R.); (S.A.)
| | - Matteo Poddighe
- Laboratory of Materials Science and Nanotechnology (LMNT), Department of Chemistry and Pharmacy, University of Sassari, CR-INSTM, Via Vienna, 2, 07100 Sassari, Italy;
| | - Santiago Aparicio
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain; (S.M.M.); (R.B.); (B.D.); (C.R.); (S.A.)
- Department of Chemistry, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneg 4, 6708 WE Wageningen, The Netherlands;
| | - Juan Antonio Tamayo-Ramos
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Banuelos s/n, 09001 Burgos, Spain; (S.M.M.); (R.B.); (B.D.); (C.R.); (S.A.)
- Correspondence:
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16
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Zondervan NA, Martins Dos Santos VAP, Suarez-Diez M, Saccenti E. Correction to: Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. BMC Genomics 2021; 22:384. [PMID: 34034678 PMCID: PMC8152301 DOI: 10.1186/s12864-021-07707-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, Netherlands.,LifeGlimmer GmBH, Markelstraße 38, 12163, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, Netherlands.
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17
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Laothanachareon T, Bruinsma L, Nijsse B, Schonewille T, Suarez-Diez M, Tamayo-Ramos JA, Martins dos Santos VAP, Schaap PJ. Global Transcriptional Response of Aspergillus niger to Blocked Active Citrate Export through Deletion of the Exporter Gene. J Fungi (Basel) 2021; 7:jof7060409. [PMID: 34071072 PMCID: PMC8224569 DOI: 10.3390/jof7060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus niger is the major industrial citrate producer worldwide. Export as well as uptake of citric acid are believed to occur by active, proton-dependent, symport systems. Both are major bottlenecks for industrial citrate production. Therefore, we assessed the consequences of deleting the citT gene encoding the A. niger citrate exporter, effectively blocking active citrate export. We followed the consumption of glucose and citrate as carbon sources, monitored the secretion of organic acids and carried out a thorough transcriptome pathway enrichment analysis. Under controlled cultivation conditions that normally promote citrate secretion, the knock-out strain secreted negligible amounts of citrate. Blocking active citrate export in this way led to a reduced glucose uptake and a reduced expression of high-affinity glucose transporter genes, mstG and mstH. The glyoxylate shunt was strongly activated and an increased expression of the OAH gene was observed, resulting in a more than two-fold higher concentration of oxalate in the medium. Deletion of citT did not affect citrate uptake suggesting that citrate export and citrate uptake are uncoupled from the system.
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Affiliation(s)
- Thanaporn Laothanachareon
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani 12120, Thailand
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Tom Schonewille
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials-ICCRAM, University of Burgos, 09001 Burgos, Spain;
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- LifeGlimmer GmbH, 12163 Berlin, Germany
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
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18
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Zondervan NA, Martins Dos Santos VAP, Suarez-Diez M, Saccenti E. Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. BMC Genomics 2021; 22:102. [PMID: 33541265 PMCID: PMC7860044 DOI: 10.1186/s12864-021-07388-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/13/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype. RESULTS We compared 235 Staphylococcus and 315 Streptococcus genomes based on their protein domain content. We show the relationships between protein persistence and essentiality by integrating essentiality predictions from two metabolic models and essentiality measurements from six large-scale transposon mutagenesis experiments. We identified clusters of strains within species based on proteins associated to similar biological processes. We built Random Forest classifiers that predicted the zoonotic potential. Furthermore, we identified shared attributes between of Staphylococcus aureus and Streptococcus pyogenes that allow them to cause necrotizing fasciitis. CONCLUSIONS Differences observed in clustering of strains based on functional groups of proteins correlate with phenotypes such as host tropism, capability to infect multiple hosts and drug resistance. Our method provides a solid basis towards large-scale prediction of phenotypes based on genomic information.
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Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands
- LifeGlimmer GmBH, Markelstraße 38, 12163, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands.
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19
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van Rosmalen RP, Smith RW, Martins Dos Santos VAP, Fleck C, Suarez-Diez M. Model reduction of genome-scale metabolic models as a basis for targeted kinetic models. Metab Eng 2021; 64:74-84. [PMID: 33486094 DOI: 10.1016/j.ymben.2021.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
Constraint-based, genome-scale metabolic models are an essential tool to guide metabolic engineering. However, they lack the detail and time dimension that kinetic models with enzyme dynamics offer. Model reduction can be used to bridge the gap between the two methods and allow for the integration of kinetic models into the Design-Built-Test-Learn cycle. Here we show that these reduced size models can be representative of the dynamics of the original model and demonstrate the automated generation and parameterisation of such models. Using these minimal models of metabolism could allow for further exploration of dynamic responses in metabolic networks.
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Affiliation(s)
- R P van Rosmalen
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - R W Smith
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - V A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, the Netherlands; Lifeglimmer GmbH, Berlin, Germany
| | - C Fleck
- Freiburg Center for Data Analysis and Modelling University of Freiburg Freiburg Germany; Control Theory and Systems Biology Laboratory, Department of Biosystems Science and En- gineering, ETH Zürich, Basel, Switzerland
| | - M Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, the Netherlands.
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20
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Kampers LFC, Koehorst JJ, van Heck RJA, Suarez-Diez M, Stams AJM, Schaap PJ. A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration. BMC Microbiol 2021; 21:9. [PMID: 33407113 PMCID: PMC7789669 DOI: 10.1186/s12866-020-02058-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions. RESULTS Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa. CONCLUSIONS The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.
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Affiliation(s)
- Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Ruben J A van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
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21
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Pham N, Reijnders M, Suarez-Diez M, Nijsse B, Springer J, Eggink G, Schaap PJ. Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production. Biotechnol Biofuels 2021; 14:2. [PMID: 33407779 PMCID: PMC7788717 DOI: 10.1186/s13068-020-01838-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/23/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cutaneotrichosporon oleaginosus ATCC 20509 is a fast-growing oleaginous basidiomycete yeast that is able to grow in a wide range of low-cost carbon sources including crude glycerol, a byproduct of biodiesel production. When glycerol is used as a carbon source, this yeast can accumulate more than 50% lipids (w/w) with high concentrations of mono-unsaturated fatty acids. RESULTS To increase our understanding of this yeast and to provide a knowledge base for further industrial use, a FAIR re-annotated genome was used to build a genome-scale, constraint-based metabolic model containing 1553 reactions involving 1373 metabolites in 11 compartments. A new description of the biomass synthesis reaction was introduced to account for massive lipid accumulation in conditions with high carbon-to-nitrogen (C/N) ratio in the media. This condition-specific biomass objective function is shown to better predict conditions with high lipid accumulation using glucose, fructose, sucrose, xylose, and glycerol as sole carbon source. CONCLUSION Contributing to the economic viability of biodiesel as renewable fuel, C. oleaginosus ATCC 20509 can effectively convert crude glycerol waste streams in lipids as a potential bioenergy source. Performance simulations are essential to identify optimal production conditions and to develop and fine tune a cost-effective production process. Our model suggests ATP-citrate lyase as a possible target to further improve lipid production.
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Affiliation(s)
- Nhung Pham
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Maarten Reijnders
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jan Springer
- Food and Biobased Research and AlgaePARC, Wageningen University and Research, Wageningen, the Netherlands
| | - Gerrit Eggink
- Food and Biobased Research and AlgaePARC, Wageningen University and Research, Wageningen, the Netherlands
- Bioprocess Engineering and AlgaePARC, Wageningen University and Research, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
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22
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Mollaei M, Timmers PHA, Suarez-Diez M, Boeren S, van Gelder AH, Stams AJM, Plugge CM. Comparative proteomics of Geobacter sulfurreducens PCA T in response to acetate, formate and/or hydrogen as electron donor. Environ Microbiol 2020; 23:299-315. [PMID: 33185968 PMCID: PMC7894505 DOI: 10.1111/1462-2920.15311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO2 fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO2 , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.
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Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Antonie H van Gelder
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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23
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Gaspari E, Malachowski A, Garcia-Morales L, Burgos R, Serrano L, Martins Dos Santos VAP, Suarez-Diez M. Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. NPJ Syst Biol Appl 2020; 6:33. [PMID: 33097709 PMCID: PMC7584665 DOI: 10.1038/s41540-020-00153-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 09/15/2020] [Indexed: 12/22/2022] Open
Abstract
Mycoplasma pneumoniae is a slow-growing, human pathogen that causes atypical pneumonia. Because it lacks a cell wall, many antibiotics are ineffective. Due to its reduced genome and dearth of many biosynthetic pathways, this fastidious bacterium depends on rich, undefined medium for growth, which makes large-scale cultivation challenging and expensive. To understand factors limiting growth, we developed a genome-scale, constraint-based model of M. pneumoniae called iEG158_mpn to describe the metabolic potential of this bacterium. We have put special emphasis on cell membrane formation to identify key lipid components to maximize bacterial growth. We have used this knowledge to predict essential components validated with in vitro serum-free media able to sustain growth. Our findings also show that glycolysis and lipid metabolism are much less efficient under hypoxia; these findings suggest that factors other than metabolism and membrane formation alone affect the growth of M. pneumoniae. Altogether, our modelling approach allowed us to optimize medium composition, enabled growth in defined media and streamlined operational requirements, thereby providing the basis for stable, reproducible and less expensive production.
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Affiliation(s)
- Erika Gaspari
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, the Netherlands.
| | - Antoni Malachowski
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, the Netherlands
| | - Luis Garcia-Morales
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.,Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, The Netherlands
| | - Raul Burgos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona, 08010, Spain
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, the Netherlands.,LifeGlimmer GmbH, MMarkelstrasse 38, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, the Netherlands.
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24
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Benito-Vaquerizo S, Diender M, Parera Olm I, Martins Dos Santos VAP, Schaap PJ, Sousa DZ, Suarez-Diez M. Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids. Comput Struct Biotechnol J 2020; 18:3255-3266. [PMID: 33240469 PMCID: PMC7658664 DOI: 10.1016/j.csbj.2020.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
We model a co-culture of C. autoethanogenum and C. kluyveri for syngas fermentation. Biomass species ratio affects ethanol and acetate profiles in the co-culture. The model predicts that addition of succinate increases caproate production. Genetic interventions in C. autoethanogenum could increase caproate production.
Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use of Clostridium species for the production of small organic molecules such as ethanol and acetate. The co-cultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri on syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that one strategy to optimize the production of medium-chain fatty-acids from syngas would be the addition of succinate. According to the prediction, addition of succinate would increase the pool of crotonyl-CoA and the ethanol/acetate uptake ratio in C. kluyveri, resulting in a flux of up to 60% of electrons into hexanoate. Another potential way to further optimize butyrate and hexanoate production would be an increase of C. autoethanogenum ethanol production. Blocking either acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) activity or formate transport, in the C. autoethanogenum metabolic model could potentially lead to an up to 150% increase in ethanol production.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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25
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Laguna-Teno F, Suarez-Diez M, Tamayo-Ramos JA. Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials. Front Microbiol 2020; 11:1943. [PMID: 32849484 PMCID: PMC7431627 DOI: 10.3389/fmicb.2020.01943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
Graphene oxide has become a very appealing nanomaterial during the last years for many different applications, but its possible impact in different biological systems remains unclear. Here, an assessment to understand the toxicity of different commercial graphene oxide nanomaterials on the unicellular fungal model organism Saccharomyces cerevisiae was performed. For this task, an RNA purification protocol was optimized to avoid the high nucleic acid absorption capacity of graphene oxide. The developed protocol is based on a sorbitol gradient separation process for the isolation of adequate ribonucleic acid levels (in concentration and purity) from yeast cultures exposed to the carbon derived nanomaterial. To pinpoint potential toxicity mechanisms and pathways, the transcriptome of S. cerevisiae exposed to 160 mg L–1 of monolayer graphene oxide (GO) and graphene oxide nanocolloids (GOC) was studied and compared. Both graphene oxide products induced expression changes in a common group of genes (104), many of them related to iron homeostasis, starvation and stress response, amino acid metabolism and formate catabolism. Also, a high number of genes were only differentially expressed in either GO (236) or GOC (1077) exposures, indicating that different commercial products can induce specific changes in the physiological state of the fungus.
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Affiliation(s)
- Felix Laguna-Teno
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
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26
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León-Saiki GM, Carreres BM, Remmers IM, Wijffels RH, Martins dos Santos VA, van der Veen D, Schaap PJ, Suarez-Diez M, Martens DE. Evaluation of diurnal responses of Tetradesmus obliquus under nitrogen limitation. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Odoni DI, Vazquez-Vilar M, van Gaal MP, Schonewille T, Martins Dos Santos VAP, Tamayo-Ramos JA, Suarez-Diez M, Schaap PJ. Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions. FEMS Microbiol Lett 2020; 366:5437674. [PMID: 31062025 PMCID: PMC6502548 DOI: 10.1093/femsle/fnz071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023] Open
Abstract
Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Merlijn P van Gaal
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom Schonewille
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Juan Antonio Tamayo-Ramos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,International Research Center in Critical Raw Materials-ICCRAM, Advanced Materials, Nuclear Technology and Applied Bio/Nanotechnology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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28
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Suarez-Diez M, Porras S, Laguna-Teno F, Schaap PJ, Tamayo-Ramos JA. Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets. Sci Rep 2020; 10:3232. [PMID: 32094381 PMCID: PMC7039959 DOI: 10.1038/s41598-020-60101-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
Graphene nanomaterials have attracted a great interest during the last years for different applications, but their possible impact on different biological systems remains unclear. Here, an assessment to understand the toxicity of commercial polycarboxylate functionalized graphene nanoplatelets (GN) on the unicellular fungal model Saccharomyces cerevisiae was performed. While cell proliferation was not negatively affected even in the presence of 800 mg L-1 of the nanomaterial for 24 hours, oxidative stress was induced at a lower concentration (160 mg L-1), after short exposure periods (2 and 4 hours). No DNA damage was observed under a comet assay analysis under the studied conditions. In addition, to pinpoint the molecular mechanisms behind the early oxidative damage induced by GN and to identify possible toxicity pathways, the transcriptome of S. cerevisiae exposed to 160 and 800 mg L-1 of GN was studied. Both GN concentrations induced expression changes in a common group of genes (337), many of them related to the fungal response to reduce the nanoparticles toxicity and to maintain cell homeostasis. Also, a high number of genes were only differentially expressed in the GN800 condition (3254), indicating that high GN concentrations can induce severe changes in the physiological state of the yeast.
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Affiliation(s)
- Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneg, 4 6708WE, Wageningen, The Netherlands
| | - Santiago Porras
- Departamento de Economía Aplicada, University of Burgos, Plaza Infanta Doña Elena, s/n, 09001, Burgos, Spain
| | - Felix Laguna-Teno
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneg, 4 6708WE, Wageningen, The Netherlands
| | - Juan A Tamayo-Ramos
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain.
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29
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Benis N, Wells JM, Smits MA, Kar SK, van der Hee B, Dos Santos VAPM, Suarez-Diez M, Schokker D. High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. BMC Genomics 2019; 20:1028. [PMID: 31888466 PMCID: PMC6937694 DOI: 10.1186/s12864-019-6390-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/12/2019] [Indexed: 12/25/2022] Open
Abstract
Background The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we performed a high-level data integration of 14 whole-genome transcriptomics datasets from samples of intestinal mouse mucosa. We used the tool Centrality based Pathway Analysis (CePa), along with information from the Reactome database. Results The results show an integrated response of the mouse intestinal mucosa to challenges with agents introduced orally that were expected to perturb homeostasis. We observed that a common set of pathways respond to different stimuli, of which the most reactive was the Regulation of Complement Cascade pathway. Altered expression of the Regulation of Complement Cascade pathway was verified in mouse organoids challenged with different stimuli in vitro. Conclusions Results of the integrated transcriptomics analysis and data driven experiment suggest an important role of epithelial production of complement and host complement defence factors in the maintenance of homeostasis.
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Affiliation(s)
- Nirupama Benis
- Host Microbe Interactomics, Wageningen University & Research, Wageningen, The Netherlands. .,Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Jerry M Wells
- Host Microbe Interactomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mari A Smits
- Host Microbe Interactomics, Wageningen University & Research, Wageningen, The Netherlands.,Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands.,Wageningen Bioveterinary Research, Wageningen University, Wageningen, The Netherlands
| | - Soumya Kanti Kar
- Host Microbe Interactomics, Wageningen University & Research, Wageningen, The Netherlands.,Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Bart van der Hee
- Host Microbe Interactomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.,LifeGlimmer GmbH, Berlin, Germany
| | - Maria Suarez-Diez
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
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Kampers LFC, van Heck RGA, Donati S, Saccenti E, Volkers RJM, Schaap PJ, Suarez-Diez M, Nikel PI, Martins Dos Santos VAP. In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions. Microb Cell Fact 2019; 18:179. [PMID: 31640713 PMCID: PMC6805499 DOI: 10.1186/s12934-019-1227-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/09/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Pseudomonas putida is a metabolically versatile, genetically accessible, and stress-robust species with outstanding potential to be used as a workhorse for industrial applications. While industry recognises the importance of robustness under micro-oxic conditions for a stable production process, the obligate aerobic nature of P. putida, attributed to its inability to produce sufficient ATP and maintain its redox balance without molecular oxygen, severely limits its use for biotechnology applications. RESULTS Here, a combination of genome-scale metabolic modelling and comparative genomics is used to pinpoint essential [Formula: see text]-dependent processes. These explain the inability of the strain to grow under anoxic conditions: a deficient ATP generation and an inability to synthesize essential metabolites. Based on this, several P. putida recombinant strains were constructed harbouring acetate kinase from Escherichia coli for ATP production, and a class I dihydroorotate dehydrogenase and a class III anaerobic ribonucleotide triphosphate reductase from Lactobacillus lactis for the synthesis of essential metabolites. Initial computational designs were fine-tuned by means of adaptive laboratory evolution. CONCLUSIONS We demonstrated the value of combining in silico approaches, experimental validation and adaptive laboratory evolution for microbial design by making the strictly aerobic Pseudomonas putida able to grow under micro-oxic conditions.
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Affiliation(s)
- Linde F C Kampers
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruben G A van Heck
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Stefano Donati
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Edoardo Saccenti
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Rita J M Volkers
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Kgs Lyngby, Denmark
| | - Vitor A P Martins Dos Santos
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands. .,LifeGlimmer GmbH, Berlin, Germany.
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Rienksma RA, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Modeling Host-Pathogen Interaction to Elucidate the Metabolic Drug Response of Intracellular Mycobacterium tuberculosis. Front Cell Infect Microbiol 2019; 9:144. [PMID: 31139575 PMCID: PMC6519342 DOI: 10.3389/fcimb.2019.00144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/17/2019] [Indexed: 12/19/2022] Open
Abstract
Little is known about the metabolic state of Mycobacterium tuberculosis (Mtb) inside the phagosome, a compartment inside phagocytes for killing pathogens and other foreign substances. We have developed a combined model of Mtb and human metabolism, sMtb-RECON and used this model to predict the metabolic state of Mtb during infection of the host. Amino acids are predicted to be used for energy production as well as biomass formation. Subsequently we assessed the effect of increasing dosages of drugs targeting metabolism on the metabolic state of the pathogen and predict resulting metabolic adaptations and flux rerouting through various pathways. In particular, the TCA cycle becomes more important upon drug application, as well as alanine, aspartate, glutamate, proline, arginine and porphyrin metabolism, while glycine, serine, and threonine metabolism become less important. We modeled the effect of 11 metabolically active drugs. Notably, the effect of eight could be recreated and two major profiles of the metabolic state were predicted. The profiles of the metabolic states of Mtb affected by the drugs BTZ043, cycloserine and its derivative terizidone, ethambutol, ethionamide, propionamide, and isoniazid were very similar, while TMC207 is predicted to have quite a different effect on metabolism as it inhibits ATP synthase and therefore indirectly interferes with a multitude of metabolic pathways.
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Affiliation(s)
- Rienk A Rienksma
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands.,LifeGlimmer GmbH, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
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Koehorst JJ, van Dam JCJ, Saccenti E, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ. SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles. Bioinformatics 2019; 34:1401-1403. [PMID: 29186322 PMCID: PMC5905645 DOI: 10.1093/bioinformatics/btx767] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022] Open
Abstract
Summary To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyze existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies. This greatly reduces the administrative burden of handling multiple analysis tools and versions thereof and facilitates multi-level large scale comparative analysis. Availability and implementation SAPP is written in JAVA and freely available at https://gitlab.com/sapp and runs on Unix-like operating systems. The documentation, examples and a tutorial are available at https://sapp.gitlab.io.
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Affiliation(s)
- Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Jesse C J van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands.,LifeGlimmer GmbH, 12163 Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
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Borewicz K, Suarez-Diez M, Hechler C, Beijers R, de Weerth C, Arts I, Penders J, Thijs C, Nauta A, Lindner C, Van Leusen E, Vaughan EE, Smidt H. The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life. Sci Rep 2019; 9:2434. [PMID: 30792412 PMCID: PMC6385197 DOI: 10.1038/s41598-018-38268-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/19/2018] [Indexed: 01/15/2023] Open
Abstract
Gastrointestinal (GI) microbiota composition differs between breastfed and formula-fed infants. Today's infant formulas are often fortified with prebiotics to better mimic properties of human milk with respect to its effect on GI microbiota composition and function. We used Illumina HiSeq sequencing of PCR-amplified 16S rRNA gene fragments to investigate the composition of faecal microbiota in 2-12 week old infants receiving either breastmilk, infant formulas fortified with prebiotics, or mixed feeding. We compared these results with results from infants fed traditional formulas used in the Netherlands in 2002-2003, which contained no added prebiotics. We showed that today's formulas supplemented with either scGOS (0.24-0.50 g/100 ml) or scGOS and lcFOS (at a 9:1 ratio; total 0.6 g/100 ml) had a strong bifidogenic effect as compared to traditional formulas, and they also resulted in altered patterns of microbial colonisation within the developing infant gastrointestinal tract. We identified three microbial states (or developmental stages) in the first 12 weeks of life, with a gradual transition pattern towards a bifidobacteria dominated state. In infants receiving only fortified formulas, this transition towards the bifidobacteria dominated state was accelerated, whereas in infants receiving mixed feeding the transition was delayed, as compared to exclusively breastfed infants.
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Affiliation(s)
- Klaudyna Borewicz
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen & Research University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christine Hechler
- Behavioral Science Institute, Radboud University, Montessorilaan 3, 6525 HR, Nijmegen, The Netherlands
| | - Roseriet Beijers
- Behavioral Science Institute, Radboud University, Montessorilaan 3, 6525 HR, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Kapittelweg 29, 6525 EN, Nijmegen, The Netherlands
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Kapittelweg 29, 6525 EN, Nijmegen, The Netherlands
| | - Ilja Arts
- Department of Epidemiology, Maastricht University, Care and Public Health Research Institute, Minderbroedersberg 4-6, 6211 LK, Maastricht, The Netherlands
- CARIM School for Cardiovascular Diseases, Universiteitssingel 50 6229ER Maastricht; and Maastricht Center for Systems Biology (MaCSBio), Universiteitssingel 60, 6229 ER, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Center, P. Debyelaan 25, 6229HX, Maastricht, The Netherlands
- NUTRIM School for Nutrition, Toxicology and Metabolism, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Carel Thijs
- Department of Epidemiology, Maastricht University, Care and Public Health Research Institute, Minderbroedersberg 4-6, 6211 LK, Maastricht, The Netherlands
| | - Arjen Nauta
- FrieslandCampina, Stationsplein 4, 3818 LE, Amersfoort, The Netherlands
| | - Cordula Lindner
- FrieslandCampina, Stationsplein 4, 3818 LE, Amersfoort, The Netherlands
| | - Ellen Van Leusen
- FrieslandCampina, Stationsplein 4, 3818 LE, Amersfoort, The Netherlands
| | - Elaine E Vaughan
- Sensus B.V. (Royal Cosun), Borchwerf 3, 4704 RG, Roosendaal, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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Jahagirdar S, Suarez-Diez M, Saccenti E. Simulation and Reconstruction of Metabolite-Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms. J Proteome Res 2019; 18:1099-1113. [PMID: 30663881 DOI: 10.1021/acs.jproteome.8b00781] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biological networks play a paramount role in our understanding of complex biological phenomena, and metabolite-metabolite association networks are now commonly used in metabolomics applications. In this study we evaluate the performance of several network inference algorithms (PCLRC, MRNET, GENIE3, TIGRESS, and modifications of the MRNET algorithm, together with standard Pearson's and Spearman's correlation) using as a test case data generated using a dynamic metabolic model describing the metabolism of arachidonic acid (consisting of 83 metabolites and 131 reactions) and simulation individual metabolic profiles of 550 subjects. The quality of the reconstructed metabolite-metabolite association networks was assessed against the original metabolic network taking into account different degrees of association among the metabolites and different sample sizes and noise levels. We found that inference algorithms based on resampling and bootstrapping perform better when correlations are used as indexes to measure the strength of metabolite-metabolite associations. We also advocate for the use of data generated using dynamic models to test the performance of algorithms for network inference since they produce correlation patterns that are more similar to those observed in real metabolomics data.
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Affiliation(s)
- Sanjeevan Jahagirdar
- Laboratory of Systems and Synthetic Biology , Wageningen University & Research , Stippeneng 4 , 6708WE Wageningen , The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology , Wageningen University & Research , Stippeneng 4 , 6708WE Wageningen , The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology , Wageningen University & Research , Stippeneng 4 , 6708WE Wageningen , The Netherlands
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Lindfors E, van Dam JCJ, Lam CMC, Zondervan NA, Martins dos Santos VAP, Suarez-Diez M. SyNDI: synchronous network data integration framework. BMC Bioinformatics 2018; 19:403. [PMID: 30400817 PMCID: PMC6219086 DOI: 10.1186/s12859-018-2426-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/10/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representing biomolecules as nodes and their interactions as edges. Very often the input data come from various sorts of omics analyses. Those resulting networks sometimes describe a wide range of aspects, for example different experiment conditions, species, tissue types, stimulating factors, mutants, or simply distinct interaction features of the same network produced by different algorithms. For these scenarios, synchronous visualization of more than one distinct network is an excellent mean to explore all the relevant networks efficiently. In addition, complementary analysis methods are needed and they should work in a workflow manner in order to gain maximal biological insights. RESULTS In order to address the aforementioned needs, we have developed a Synchronous Network Data Integration (SyNDI) framework. This framework contains SyncVis, a Cytoscape application for user-friendly synchronous and simultaneous visualization of multiple biological networks, and it is seamlessly integrated with other bioinformatics tools via the Galaxy platform. We demonstrated the functionality and usability of the framework with three biological examples - we analyzed the distinct connectivity of plasma metabolites in networks associated with high or low latent cardiovascular disease risk; deeper insights were obtained from a few similar inflammatory response pathways in Staphylococcus aureus infection common to human and mouse; and regulatory motifs which have not been reported associated with transcriptional adaptations of Mycobacterium tuberculosis were identified. CONCLUSIONS Our SyNDI framework couples synchronous network visualization seamlessly with additional bioinformatics tools. The user can easily tailor the framework for his/her needs by adding new tools and datasets to the Galaxy platform.
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Affiliation(s)
- Erno Lindfors
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany
| | - Jesse C. J. van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Niels A. Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A. P. Martins dos Santos
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Wegrzyn AB, Stolle S, Rienksma RA, Martins Dos Santos VAP, Bakker BM, Suarez-Diez M. Cofactors revisited - Predicting the impact of flavoprotein-related diseases on a genome scale. Biochim Biophys Acta Mol Basis Dis 2018; 1865:360-370. [PMID: 30385409 DOI: 10.1016/j.bbadis.2018.10.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/10/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022]
Abstract
Flavin adenine dinucleotide (FAD) and its precursor flavin mononucleotide (FMN) are redox cofactors that are required for the activity of more than hundred human enzymes. Mutations in the genes encoding these proteins cause severe phenotypes, including a lack of energy supply and accumulation of toxic intermediates. Ideally, patients should be diagnosed before they show symptoms so that treatment and/or preventive care can start immediately. This can be achieved by standardized newborn screening tests. However, many of the flavin-related diseases lack appropriate biomarker profiles. Genome-scale metabolic models can aid in biomarker research by predicting altered profiles of potential biomarkers. Unfortunately, current models, including the most recent human metabolic reconstructions Recon and HMR, typically treat enzyme-bound flavins incorrectly as free metabolites. This in turn leads to artificial degrees of freedom in pathways that are strictly coupled. Here, we present a reconstruction of human metabolism with a curated and extended flavoproteome. To illustrate the functional consequences, we show that simulations with the curated model - unlike simulations with earlier Recon versions - correctly predict the metabolic impact of multiple-acyl-CoA-dehydrogenase deficiency as well as of systemic flavin-depletion. Moreover, simulations with the new model allowed us to identify a larger number of biomarkers in flavoproteome-related diseases, without loss of accuracy. We conclude that adequate inclusion of cofactors in constraint-based modelling contributes to higher precision in computational predictions.
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Affiliation(s)
- Agnieszka B Wegrzyn
- Systems Medicine of Metabolism and Signaling, Laboratory of Pediatrics, University Medical Center Groningen, University of Groningen, 9713, AV, Groningen, the Netherlands; Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, 9713, AV, Groningen, the Netherlands
| | - Sarah Stolle
- Systems Medicine of Metabolism and Signaling, Laboratory of Pediatrics, University Medical Center Groningen, University of Groningen, 9713, AV, Groningen, the Netherlands; Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, 9713, AV, Groningen, the Netherlands
| | - Rienk A Rienksma
- Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands
| | - Vítor A P Martins Dos Santos
- Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands; Lifeglimmer GmbH., 12163 Berlin, Germany
| | - Barbara M Bakker
- Systems Medicine of Metabolism and Signaling, Laboratory of Pediatrics, University Medical Center Groningen, University of Groningen, 9713, AV, Groningen, the Netherlands; Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, 9713, AV, Groningen, the Netherlands.
| | - Maria Suarez-Diez
- Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands.
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Rienksma RA, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection. Front Cell Infect Microbiol 2018; 8:264. [PMID: 30123778 PMCID: PMC6085482 DOI: 10.3389/fcimb.2018.00264] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/13/2018] [Indexed: 01/15/2023] Open
Abstract
Genome-scale metabolic models of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, have been envisioned as a platform for drug discovery. By systematically probing the networks that underpin such models, the reactions that are essential for Mtb are identified. A majority of these reactions are catalyzed by enzymes and thus represent candidate drug targets to fight an Mtb infection. Nevertheless, this is complicated by the limited knowledge on the environment that Mtb encounters during infection. Modeling the behavior of the bacteria during infection requires knowledge of the so-called biomass reaction that represents bacterial biomass composition. This composition varies in different environments or bacterial growth phases. Accurate modeling of the metabolic state requires a precise biomass reaction for the described condition. In recent years, additional insights in the in-host environment occupied by Mtb have been gained as transcript abundance data of interacting host and pathogen have become available. Therefore, we used transcript abundance data and developed a straightforward and systematic method to obtain a condition-specific biomass reaction for Mtb during in vitro growth and during infection of its host. The method described herein is virtually free of any pre-set assumptions on uptake rates of nutrients, making it suitable for exploring environments with limited accessibility. The condition-specific biomass reaction represents the “metabolic objective” of Mtb in a given environment (in-host growth and growth on defined medium) at a specific time point, and as such allows modeling the bacterial metabolic state in these environments. Five different biomass reactions were used to predict nutrient uptake rates and gene essentiality. Predictions were subsequently compared to available experimental data. Our results show that nutrient uptake can accurately be predicted. Gene essentiality can also be predicted but accurate predictions remain difficult to obtain. In conclusion, a viable strategy to model Mtb metabolism in hard-to-access environments that is virtually free of pre-set assumptions is provided.
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Affiliation(s)
- Rienk A Rienksma
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
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Sinha N, Suarez-Diez M, Hooiveld GJEJ, Keijer J, Martin Dos Santos V, van Schothorst EM. A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load. Front Physiol 2018; 9:749. [PMID: 29962969 PMCID: PMC6013923 DOI: 10.3389/fphys.2018.00749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/28/2018] [Indexed: 12/12/2022] Open
Abstract
Computational modeling of mitochondrial adaptability and flexibility in the small intestine upon different nutritional exposures will provide insights that will help to define healthy diet interventions. Therefore, a murine enterocyte-specific mitochondrial constraint-based metabolic model (named MT_mmuENT127) was constructed and used to simulate mitochondrial behavior under different dietary conditions, representing various levels and composition of nutrients absorbed by the enterocytes in mice, primarily focusing on metabolic pathways. Our simulations predicted that increasing the fraction of marine fatty acids in the diet, or increasing the dietary lipid/carbohydrate ratio resulted in (i) an increase in mitochondrial fatty acid beta oxidation, and (ii) changes in only a limited subset of mitochondrial reactions, which appeared to be independent of gene expression regulation. Moreover, transcript levels of mitochondrial proteins suggested unaltered fusion–fission dynamics by an increased lipid/carbohydrates ratio or by increased fractions of marine fatty acids. In conclusion, our enterocytic mitochondrial constraint-based model was shown to be a suitable platform to investigate effects of dietary interventions on mitochondrial adaptation and provided novel and deeper insights in mitochondrial metabolism and regulation.
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Affiliation(s)
- Neeraj Sinha
- Nutrition, Metabolism and Genomics, Division of Human Nutrition, Wageningen University & Research, Wageningen, Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands.,Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics, Division of Human Nutrition, Wageningen University & Research, Wageningen, Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Vitor Martin Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands.,LifeGlimmer GmbH, Berlin, Germany
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Subramanian K, Góra A, Spruijt R, Mitusińska K, Suarez-Diez M, Martins dos Santos V, Schaap PJ. Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS One 2018; 13:e0198990. [PMID: 29906280 PMCID: PMC6003678 DOI: 10.1371/journal.pone.0198990] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 11/28/2022] Open
Abstract
D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.
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Affiliation(s)
- Kalyanasundaram Subramanian
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
| | - Ruud Spruijt
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
- Department of Chemistry, Silesian University of Technology, ks. Marcina Strzody, Gliwice, Poland
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
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van der Ark KCH, Aalvink S, Suarez-Diez M, Schaap PJ, de Vos WM, Belzer C. Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation. Microb Biotechnol 2018; 11:476-485. [PMID: 29377524 PMCID: PMC5902328 DOI: 10.1111/1751-7915.13033] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 02/04/2023] Open
Abstract
The abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A. muciniphila is known to use mucin as sole carbon and nitrogen source. To study the physiology and the potential for therapeutic applications of this bacterium, we designed a defined minimal medium. The composition of the medium was based on the genome‐scale metabolic model of A. muciniphila and the composition of mucin. Our results indicate that A. muciniphila does not code for GlmS, the enzyme that mediates the conversion of fructose‐6‐phosphate (Fru6P) to glucosamine‐6‐phosphate (GlcN6P), which is essential in peptidoglycan formation. The only annotated enzyme that could mediate this conversion is Amuc‐NagB on locus Amuc_1822. We found that Amuc‐NagB was unable to form GlcN6P from Fru6P at physiological conditions, while it efficiently catalyzed the reverse reaction. To overcome this inability, N‐acetylglucosamine needs to be present in the medium for A. muciniphila growth. With these findings, the genome‐scale metabolic model was updated and used to accurately predict growth of A. muciniphila on synthetic media. The finding that A. muciniphila has a necessity for GlcNAc, which is present in mucin further prompts the adaptation to its mucosal niche.
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Affiliation(s)
- Kees C H van der Ark
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Department of Bacteriology and Immunology, RPU Immunobiology, University of Helsinki, Haartmanikatu 4, 002940, Helsinki, Finland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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41
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Zondervan NA, van Dam JCJ, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story. Int J Mol Sci 2018; 19:E347. [PMID: 29364195 PMCID: PMC5855569 DOI: 10.3390/ijms19020347] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review recent literature to provide a systems level overview of the molecular and cellular components involved in divalent metal homeostasis and their role in regulating the three main virulence strategies of M. tuberculosis: immune modulation, dormancy and phagosomal rupture. We provide a visual and modular overview of these components and their regulation. Our analysis identified a single regulatory cascade for these three virulence strategies that respond to limited availability of divalent metals in the phagosome.
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Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Jesse C J van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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42
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Odoni DI, van Gaal MP, Schonewille T, Tamayo-Ramos JA, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ. Aspergillus niger Secretes Citrate to Increase Iron Bioavailability. Front Microbiol 2017; 8:1424. [PMID: 28824560 PMCID: PMC5539119 DOI: 10.3389/fmicb.2017.01424] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 11/13/2022] Open
Abstract
Aspergillus niger has an innate ability to secrete various organic acids, including citrate. The conditions required for A. niger citrate overproduction are well described, but the physiological reasons underlying extracellular citrate accumulation are not yet fully understood. One of the less understood culture conditions is the requirement of growth-limiting iron concentrations. While this has been attributed to iron-dependent citrate metabolizing enzymes, this straightforward relationship does not always hold true. Here, we show that an increase in citrate secretion under iron limited conditions is a physiological response consistent with a role of citrate as A. niger iron siderophore. We found that A. niger citrate secretion increases with decreasing amounts of iron added to the culture medium and, in contrast to previous findings, this response is independent of the nitrogen source. Differential transcriptomics analyses of the two A. niger mutants NW305 (gluconate non-producer) and NW186 (gluconate and oxalate non-producer) revealed up-regulation of the citrate biosynthesis gene citA under iron limited conditions compared to iron replete conditions. In addition, we show that A. niger can utilize Fe(III) citrate as iron source. Finally, we discuss our findings in the general context of the pH-dependency of A. niger organic acid production, offering an explanation, besides competition, for why A. niger organic acid production is a sequential process influenced by the external pH of the culture medium.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Merlijn P van Gaal
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands.,Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Tom Schonewille
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Juan A Tamayo-Ramos
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands.,LifeGlimmer GmBHBerlin, Germany
| | - Maria Suarez-Diez
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Peter J Schaap
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
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43
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Venkatasubramanian PB, Toydemir G, de Wit N, Saccenti E, Martins Dos Santos VAP, van Baarlen P, Wells JM, Suarez-Diez M, Mes JJ. Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity. Sci Rep 2017; 7:6778. [PMID: 28755007 PMCID: PMC5533711 DOI: 10.1038/s41598-017-06355-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/09/2017] [Indexed: 12/30/2022] Open
Abstract
Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever been initiated and Caco-2-dedicated gene expression networks are barely available. Here, 341 Caco-2-specific microarray samples were collected from public databases and from in-house experiments pertaining to Caco-2 cells exposed to pathogens, probiotics and several food compounds. Using these datasets, a gene functional association network specific for Caco-2 was generated containing 8937 nodes 129711 edges. Two in silico methods, a modified version of biclustering and the new Differential Expression Correlation Analysis, were developed to identify Caco-2-specific gene targets within a pathway of interest. These methods were subsequently applied to the AhR and Nrf2 signalling pathways and altered expression of the predicted target genes was validated by qPCR in Caco-2 cells exposed to coffee extracts, known to activate both AhR and Nrf2 pathways. The datasets and in silico method(s) to identify and predict responsive target genes can be used to more efficiently design experiments to study Caco-2/intestinal epithelial-relevant biological processes.
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Affiliation(s)
| | - Gamze Toydemir
- Alanya Alaaddin Keykubat University, Faculty of Engineering, Food Engineering Department, Kestel-Alanya, 07450, Antalya, Turkey
| | - Nicole de Wit
- Wageningen University & Research, Food & Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Edoardo Saccenti
- Wageningen University & Research, Systems and Synthetic Biology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Wageningen University & Research, Systems and Synthetic Biology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,LifeGlimmerGmbH, Markelstrasse 38, 12163, Berlin, Germany
| | - Peter van Baarlen
- Wageningen University & Research, Host-Microbe Interactomics, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Jerry M Wells
- Wageningen University & Research, Host-Microbe Interactomics, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Wageningen University & Research, Systems and Synthetic Biology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jurriaan J Mes
- Wageningen University & Research, Food & Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands.
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44
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Kamminga T, Slagman SJ, Bijlsma JJE, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ. Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate. Biotechnol Bioeng 2017; 114:2339-2347. [PMID: 28600895 PMCID: PMC6084303 DOI: 10.1002/bit.26347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/13/2017] [Accepted: 06/07/2017] [Indexed: 11/08/2022]
Abstract
Mycoplasma hyopneumoniae is cultured on large-scale to produce antigen for inactivated whole-cell vaccines against respiratory disease in pigs. However, the fastidious nutrient requirements of this minimal bacterium and the low growth rate make it challenging to reach sufficient biomass yield for antigen production. In this study, we sequenced the genome of M. hyopneumoniae strain 11 and constructed a high quality constraint-based genome-scale metabolic model of 284 chemical reactions and 298 metabolites. We validated the model with time-series data of duplicate fermentation cultures to aim for an integrated model describing the dynamic profiles measured in fermentations. The model predicted that 84% of cellular energy in a standard M. hyopneumoniae cultivation was used for non-growth associated maintenance and only 16% of cellular energy was used for growth and growth associated maintenance. Following a cycle of model-driven experimentation in dedicated fermentation experiments, we were able to increase the fraction of cellular energy used for growth through pyruvate addition to the medium. This increase in turn led to an increase in growth rate and a 2.3 times increase in the total biomass concentration reached after 3-4 days of fermentation, enhancing the productivity of the overall process. The model presented provides a solid basis to understand and further improve M. hyopneumoniae fermentation processes. Biotechnol. Bioeng. 2017;114: 2339-2347. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tjerko Kamminga
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, 6708, Wageningen, The Netherlands.,Bioprocess Technology and Support, MSD Animal Health, Boxmeer, The Netherlands
| | - Simen-Jan Slagman
- Bioprocess Technology and Support, MSD Animal Health, Boxmeer, The Netherlands
| | - Jetta J E Bijlsma
- Discovery and Technology, MSD Animal Health, Boxmeer, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, 6708, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, 6708, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, 6708, Wageningen, The Netherlands
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45
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Benis N, Kar SK, Martins Dos Santos VAP, Smits MA, Schokker D, Suarez-Diez M. Multi-Level Integration of Environmentally Perturbed Internal Phenotypes Reveals Key Points of Connectivity between Them. Front Physiol 2017; 8:388. [PMID: 28659815 PMCID: PMC5467433 DOI: 10.3389/fphys.2017.00388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/23/2017] [Indexed: 12/21/2022] Open
Abstract
The genotype and external phenotype of organisms are linked by so-called internal phenotypes which are influenced by environmental conditions. In this study, we used five existing -omics datasets representing five different layers of internal phenotypes, which were simultaneously measured in dietarily perturbed mice. We performed 10 pair-wise correlation analyses verified with a null model built from randomized data. Subsequently, the inferred networks were merged and literature mined for co-occurrences of identified linked nodes. Densely connected internal phenotypes emerged. Forty-five nodes have links with all other data-types and we denote them “connectivity hubs.” In literature, we found proof of 6% of the 577 connections, suggesting a biological meaning for the observed correlations. The observed connectivities between metabolite and cytokines hubs showed higher numbers of literature hits as compared to the number of literature hits on the connectivities between the microbiota and gene expression internal phenotypes. We conclude that multi-level integrated networks may help to generate hypotheses and to design experiments aiming to further close the gap between genotype and phenotype. We describe and/or hypothesize on the biological relevance of four identified multi-level connectivity hubs.
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Affiliation(s)
- Nirupama Benis
- Host Microbe Interactomics, Wageningen University & ResearchWageningen, Netherlands
| | - Soumya K Kar
- Host Microbe Interactomics, Wageningen University & ResearchWageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & ResearchWageningen, Netherlands.,Lifeglimmer GmbHBerlin, Germany
| | - Mari A Smits
- Wageningen Livestock Research, Wageningen University & ResearchWageningen, Netherlands.,Wageningen Bioveterinary Research, Wageningen University & ResearchWageningen, Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University & ResearchWageningen, Netherlands
| | - Maria Suarez-Diez
- Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & ResearchWageningen, Netherlands
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46
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Suarez-Diez M, Adam J, Adamski J, Chasapi SA, Luchinat C, Peters A, Prehn C, Santucci C, Spyridonidis A, Spyroulias GA, Tenori L, Wang-Sattler R, Saccenti E. Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling. J Proteome Res 2017; 16:2547-2559. [PMID: 28517934 PMCID: PMC5645760 DOI: 10.1021/acs.jproteome.7b00106] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Blood is one of the most used biofluids
in metabolomics studies,
and the serum and plasma fractions are routinely used as a proxy for
blood itself. Here we investigated the association networks of an
array of 29 metabolites identified and quantified via NMR in the plasma
and serum samples of two cohorts of ∼1000 healthy blood donors
each. A second study of 377 individuals was used to extract plasma
and serum samples from the same individual on which a set of 122 metabolites
were detected and quantified using FIA–MS/MS. Four different
inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain
consensus networks. The plasma and serum networks obtained from different
studies showed different topological properties with the serum network
being more connected than the plasma network. On a global level, metabolite
association networks from plasma and serum fractions obtained from
the same blood sample of healthy people show similar topologies, and
at a local level, some differences arise like in the case of amino
acids.
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Affiliation(s)
- Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jonathan Adam
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Experimental Genetics, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München , 85353 Freising, Germany
| | | | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Department of Environmental Health, Harvard School of Public Health , Boston, Massachusetts 02115, United States
| | - Cornelia Prehn
- Institute of Experimental Genetics, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany
| | - Claudio Santucci
- Magnetic Resonance Center (CERM), University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | | | | | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence , Largo Brambilla 3, 501134 Florence, Italy
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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47
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Odoni DI, Tamayo-Ramos JA, Sloothaak J, van Heck RGA, Martins Dos Santos VAP, de Graaff LH, Suarez-Diez M, Schaap PJ. Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation. PeerJ 2017; 5:e3133. [PMID: 28382234 PMCID: PMC5376114 DOI: 10.7717/peerj.3133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/01/2017] [Indexed: 11/20/2022] Open
Abstract
The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood. We set out to increase the knowledge about fumarate accumulation in R. delemar. To this end, we combined a transcriptomics and proteomics approach to identify key metabolic pathways involved in fumarate production in R. delemar, and propose that a substantial part of the fumarate accumulated in R. delemar during nitrogen starvation results from the urea cycle due to amino acid catabolism.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Juan A Tamayo-Ramos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jasper Sloothaak
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ruben G A van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.,LifeGlimmer GmBH, Berlin, Germany
| | - Leo H de Graaff
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
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48
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Koehorst JJ, van Dam JCJ, van Heck RGA, Saccenti E, dos Santos VAPM, Suarez-Diez M, Schaap PJ. Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data. Sci Rep 2016; 6:38699. [PMID: 27922098 PMCID: PMC5138606 DOI: 10.1038/srep38699] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/14/2016] [Indexed: 11/08/2022] Open
Abstract
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
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Affiliation(s)
- Jasper J. Koehorst
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
| | - Jesse C. J. van Dam
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
| | - Ruben G. A. van Heck
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
| | - Edoardo Saccenti
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
| | - Vitor A. P. Martins dos Santos
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Maria Suarez-Diez
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
| | - Peter J. Schaap
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands
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49
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Nobrega FL, Ferreira D, Martins IM, Suarez-Diez M, Azeredo J, Kluskens LD, Rodrigues LR. Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies. BMC Cancer 2016; 16:881. [PMID: 27842517 PMCID: PMC5109716 DOI: 10.1186/s12885-016-2937-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/25/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Claudin-low breast carcinoma represents 19% of all breast cancer cases and is characterized by an aggressive progression with metastatic nature and high rates of relapse. Due to a lack of known specific molecular biomarkers for this breast cancer subtype, there are no targeted therapies available, which results in the worst prognosis of all breast cancer subtypes. Hence, the identification of novel biomarkers for this type of breast cancer is highly relevant for an early diagnosis. Additionally, claudin-low breast carcinoma peptide ligands can be used to design powerful drug delivery systems that specifically target this type of breast cancer. METHODS In this work, we propose the identification of peptides for the specific recognition of MDA-MB-231, a cell line representative of claudin-low breast cancers, using phage display (both conventional panning and BRASIL). Binding assays, such as phage forming units and ELISA, were performed to select the most interesting peptides (i.e., specific to the target cells) and bioinformatics approaches were applied to putatively identify the biomarkers to which these peptides bind. RESULTS Two peptides were selected using this methodology specifically targeting MDA-MB-231 cells, as demonstrated by a 4 to 9 log higher affinity as compared to control cells. The use of bioinformatics approaches provided relevant insights into possible cell surface targets for each peptide identified. CONCLUSIONS The peptides herein identified may contribute to an earlier detection of claudin-low breast carcinomas and possibly to develop more individualized therapies.
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Affiliation(s)
- Franklin L Nobrega
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Débora Ferreira
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ivone M Martins
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Joana Azeredo
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Leon D Kluskens
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Lígia R Rodrigues
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J.M. Stams A, Springael D, Dejonghe W, Smidt H. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol 2016; 19:968-981. [DOI: 10.1111/1462-2920.13531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Yue Lu
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Ying Zheng
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | | | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health; Ingolstädter Landstrasse 1 Neuherberg D-85764 Germany
| | - Alfons J.M. Stams
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
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