Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

BackgroundThe green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, this work aimed at reconstructing a carbon core metabolic network for D. salina CCAP 19/18 based on the recently published nuclear genome and its validation with experimental observations and literature data.ResultsThe reconstruction resulted in a network model with 221 reactions and 212 metabolites within three compartments: cytosol, chloroplast and mitochondrion. The network was implemented in the MATLAB toolbox CellNetAnalyzer and checked for feasibility. Furthermore, a flux balance analysis was carried out for different light and nutrient uptake rates. The comparison of the experimental knowledge with the model prediction revealed that the results of the stoichiometric network analysis are plausible and in good agreement with the observed behavior. Accordingly, our model provides an excellent tool for investigating the carbon core metabolism of D. salina.ConclusionsThe reconstructed metabolic network of D. salina presented in this work is able to predict the biological behavior under light and nutrient stress and will lead to an improved process understanding for the optimized production of high-value products in microalgae.

[1]  S. Jia,et al.  Metabolic Profiling of Dunaliella salina Shifting Cultivation Conditions toNitrogen Deprivation , 2016 .

[2]  P. Schenk,et al.  Microalgal biofactories: a promising approach towards sustainable omega-3 fatty acid production , 2012, Microbial Cell Factories.

[3]  Colin Hill,et al.  Viromes of one year old infants reveal the impact of birth mode on microbiome diversity , 2018, PeerJ.

[4]  Steffen Klamt,et al.  Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.

[5]  J. Schmutz,et al.  Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/18 , 2017, Genome Announcements.

[6]  Sascha Schäuble,et al.  A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. , 2015, The Plant journal : for cell and molecular biology.

[7]  P. Gómez,et al.  Taxonomy and Phylogeny of the Genus Dunaliella , 2009, The Alga Dunaliella.

[8]  J. Schwender,et al.  Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to ¹³C metabolic flux analysis. , 2011, The Plant journal : for cell and molecular biology.

[9]  U. Pick,et al.  Regulation of glycerol synthesis in response to osmotic changes in dunaliella. , 1991, Plant physiology.

[10]  Lake-Ee Quek,et al.  AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome , 2011, BMC Genomics.

[11]  Elias W. Krumholz,et al.  Genome-wide metabolic network reconstruction of the picoalga Ostreococcus. , 2012, Journal of experimental botany.

[12]  A. Ben‐Amotz,et al.  On the Factors Which Determine Massive beta-Carotene Accumulation in the Halotolerant Alga Dunaliella bardawil. , 1983, Plant physiology.

[13]  Björn H. Junker,et al.  Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale1[W][OPEN] , 2013, Plant Physiology.

[14]  P I Barton,et al.  A reliable simulator for dynamic flux balance analysis , 2013, Biotechnology and bioengineering.

[15]  Kai Sundmacher,et al.  Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae , 2016, Biotechnology for Biofuels.

[16]  Luis Miguel Serrano-Bermúdez,et al.  Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO2 levels , 2018, PeerJ.

[17]  K. Shimizu,et al.  Energetics and carbon metabolism during growth of microalgal cells under photoautotrophic, mixotrophic and cyclic light-autotrophic/dark-heterotrophic conditions. , 2000, Biochemical engineering journal.

[18]  Jason A. Papin,et al.  Metabolic network analysis integrated with transcript verification for sequenced genomes , 2009, Nature Methods.

[19]  John A. Morgan,et al.  BMC Systems Biology BioMed Central Research article , 2009 .

[20]  Yang Kuang,et al.  Growth and neutral lipid synthesis in green microalgae: a mathematical model. , 2011, Bioresource technology.

[21]  L. Laurens,et al.  Comparative energetics of carbon storage molecules in green algae , 2018 .

[22]  Eliza M. Wiech,et al.  Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme , 2014, Metabolites.

[23]  Carotenoid Production Process using Green Microalgae of the Dunaliella Genus: Model-Based Analysis of Interspecies Variability , 2017 .

[24]  D. Das,et al.  Flux balance analysis of Chlorella sp. FC2 IITG under photoautotrophic and heterotrophic growth conditions , 2013, Photosynthesis Research.

[25]  Yihang Zhu,et al.  Use of flux balance analysis to promote lipid productivity in Chlorella sorokiniana , 2017, Journal of Applied Phycology.

[26]  O. Bernard,et al.  Calibration of a productivity model for the microalgae Dunaliella salina accounting for light and temperature , 2017 .

[27]  Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance , 2011, Journal of Applied Phycology.

[28]  M. Borowitzka.  High-value products from microalgae—their development and commercialisation , 2013, Journal of Applied Phycology.

[29]  Michael Hippler,et al.  PredAlgo: a new subcellular localization prediction tool dedicated to green algae. , 2012, Molecular biology and evolution.

[30]  S. Mayfield,et al.  In Metabolic Engineering of Eukaryotic Microalgae: Potential and Challenges Come with Great Diversity , 2015, Front. Microbiol..

[31]  S. Mayfield,et al.  Modifications of the metabolic pathways of lipid and triacylglycerol production in microalgae , 2011, Microbial cell factories.

[32]  M. I. Khan,et al.  The promising future of microalgae: current status, challenges, and optimization of a sustainable and renewable industry for biofuels, feed, and other products , 2018, Microbial Cell Factories.

[33]  Thomas H. Bradley,et al.  Microalgae bulk growth model with application to industrial scale systems. , 2011, Bioresource technology.

[34]  Pierre Masci,et al.  Modelling neutral lipid production by the microalga Isochrysis aff. galbana under nitrogen limitation. , 2011, Bioresource technology.

[35]  René H Wijffels,et al.  Carotenoid and fatty acid metabolism in nitrogen-starved Dunaliella salina, a unicellular green microalga. , 2012, Journal of biotechnology.

[36]  P. Beyer,et al.  Induced b-Carotene Synthesis Driven by Triacylglycerol Deposition in the Unicellular Alga Dunaliella bardawil 1 , 1998 .

[37]  J. Sussman,et al.  An unusual halotolerant α-type carbonic anhydrase from the alga Dunaliella salina functionally expressed in Escherichia coli , 2003 .

[38]  B. Zielińska,et al.  Analysis of Triacylglycerols and Free Fatty Acids in Algae Using Ultra-Performance Liquid Chromatography Mass Spectrometry , 2013 .

[39]  Ruben G. A. van Heck,et al.  Green genes: bioinformatics and systems-biology innovations drive algal biotechnology. , 2014, Trends in biotechnology.

[40]  A. Elkamel,et al.  Optimization of lipid production in Chlorella vulgaris for biodiesel production using flux balance analysis , 2019, Biochemical Engineering Journal.

[41]  J. Schwartz,et al.  Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii , 2015, Front. Plant Sci..

[42]  René H Wijffels,et al.  Carotenoid and fatty acid metabolism in light‐stressed Dunaliella salina , 2010, Biotechnology and bioengineering.

[43]  Jianzhong Sun,et al.  The endophytic bacteria isolated from elephant grass (Pennisetum purpureum Schumach) promote plant growth and enhance salt tolerance of Hybrid Pennisetum , 2016, Biotechnology for Biofuels.

[44]  L. Quek,et al.  AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis1[W] , 2009, Plant Physiology.

[45]  R. Flassig,et al.  A dynamic growth model of Dunaliella salina: parameter identification and profile likelihood analysis. , 2014, Bioresource technology.

[46]  M. Borowitzka.  Commercial production of microalgae: ponds, tanks, tubes and fermenters , 1999 .

[47]  Qingyu Wu,et al.  Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides1[OPEN] , 2014, Plant Physiology.

[48]  E. Jin,et al.  The unicellular green alga Dunaliella salina Teod. as a model for abiotic stress tolerance: genetic advances and future perspectives , 2011 .

[49]  J. Moroney,et al.  The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles , 2011, Photosynthesis Research.

[50]  E. Jin,et al.  Identification of the carbonic anhydrases from the unicellular green alga Dunaliella salina strain CCAP 19/18 , 2016 .

[51]  Nicolás Loira,et al.  Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production , 2017, BMC Systems Biology.

[52]  J. Alric,et al.  Central Carbon Metabolism and Electron Transport in Chlamydomonas reinhardtii: Metabolic Constraints for Carbon Partitioning between Oil and Starch , 2013, Eukaryotic Cell.

[53]  Jason A. Papin,et al.  Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism , 2011, Molecular systems biology.

[54]  Olivier Bernard,et al.  Full-scale validation of an algal productivity model including nitrogen limitation , 2018 .