Advertisement

Algae Genome-Scale Reconstruction, Modelling and Applications

  • Cristiana G. O. Dal’Molin
  • Lars K. Nielsen
Chapter
Part of the Developments in Applied Phycology book series (DAPH, volume 6)

Abstract

Driven by revolutionary advances in high-throughput omics technologies, genome-scale metabolic reconstructions are a common denominator in systems biology and are available for a wide range of organisms. The constraint modelling formulation approach derived from the metabolic reconstructions have been successfully used to a number of applications including: metabolic engineering, biofuel research, genome functional annotation, omics data integration and in particular global pathway analysis. Recent advances have been made on plant and algae genome-scale metabolic reconstruction. In this book chapter we present the genome-scale reconstructions based on Chlamydomonas reinhardtii along with modelling formulation. We also give a few examples of the use of genome-scale models to algae biotechnological applications.

Keywords

Genome-scale reconstruction Algae metagbolism Systems biology Modelling Chlamydomonas reinhardtii 

References

  1. Blazeck J, Alper H (2010) Systems metabolic engineering: genome-scale models and beyond. Biotechnol J 5:647–659CrossRefPubMedPubMedCentralGoogle Scholar
  2. Branyikova I, Marsalkova B, Doucha J, Branyik T, Bisova K, Zachleder V, Vitova M (2011) Microalgae – novel highly efficient starch producers. Biotechnol Bioeng 108:766–776CrossRefPubMedGoogle Scholar
  3. Cakir T, Efe C, Dikicioglu D, Hortacsu A, Kirdar B, Oliver SG (2007) Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains. Biotechnol Prog 23:320–326CrossRefPubMedGoogle Scholar
  4. Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson B, Salehi-Ashtiani K, Papin JA (2011) Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol 7:518. doi: 10.1038/msb.2011.52 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Chen YH, Walker TH (2011) Biomass and lipid production of heterotrophic microalgae Chlorella protothecoides by using biodiesel-derived crude glycerol. Biotechnol Lett 33:1973–1983CrossRefPubMedGoogle Scholar
  6. Chen CY, Yeh KL, Aisyah R, Lee DJ, Chang JS (2011) Cultivation, photobioreactor design and harvesting of microalgae for biodiesel production: a critical review. Bioresour Technol 102:71–81CrossRefPubMedGoogle Scholar
  7. Chisti Y (2007) Biodiesel from microalgae. Biotechnol Adv 25:294–306CrossRefPubMedGoogle Scholar
  8. de la Rosa FF, Montes O, Galvan F (2001) Solar energy conversion by green microalgae: a photosystem for hydrogen peroxide production. Biotechnol Bioeng 74:539–543CrossRefPubMedGoogle Scholar
  9. de Oliveira Dal’Molin CG, Nielsen LK (2013) Plant genome-scale metabolic reconstruction and modelling. Curr Opin Biotechnol 24:271–277CrossRefPubMedGoogle Scholar
  10. de Oliveira Dal’Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010a) C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiol 154:1871–1885CrossRefPubMedCentralGoogle Scholar
  11. de Oliveira Dal’Molin CGD, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010b) AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol 152:579–589CrossRefPubMedPubMedCentralGoogle Scholar
  12. de Oliveira Dal’Molin CG, Quek LE, Palfreyman RW, Nielsen LK (2011) AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. BMC Genomics 12(Suppl 4):S5CrossRefGoogle Scholar
  13. de Oliveira Dal’molin CG, Quek LE, Palfreyman RW, Nielsen LK (2014) Plant genome-scale modeling and implementation. Methods Mol Biol 1090:317–332CrossRefGoogle Scholar
  14. de Oliveira Dal’Molin CG, Saa PA, Nielsen LK (2015) A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Front Plant Sci 6:4. doi: 10.3389/fpls.2015.00004 Google Scholar
  15. DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinforma 8:139CrossRefGoogle Scholar
  16. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104:1777–1782CrossRefPubMedPubMedCentralGoogle Scholar
  17. Durot M, Bourguignon PY, Schachter V (2009) Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 33:164–190CrossRefPubMedPubMedCentralGoogle Scholar
  18. Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125–130CrossRefPubMedGoogle Scholar
  19. Escobar R, Garcia-Dominguez S, Guiraum A, Montes O, Galvan F, de La Rosa FF (2000) A flow injection chemiluminescence method using Cr(III) as a catalyst for determining hydrogen peroxide. Application to H2O2 determination in cultures of microalgae. Luminescence 15:131–135CrossRefPubMedGoogle Scholar
  20. Famili I, Forster J, Nielson J, Palsson BO (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A 100:13134–13139CrossRefPubMedPubMedCentralGoogle Scholar
  21. Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7:129–143CrossRefPubMedPubMedCentralGoogle Scholar
  22. Fernandes BD, Dragone GM, Teixeira JA, Vicente AA (2010) Light regime characterization in an airlift photobioreactor for production of microalgae with high starch content. Appl Biochem Biotechnol 161:218–226CrossRefPubMedGoogle Scholar
  23. Forster J, Famili I, Fu P, Palsson BO, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13:244–253CrossRefPubMedPubMedCentralGoogle Scholar
  24. Goh LP Jr, Loh SP, Fatimah MY, Perumal K (2009) bioaccessibility of carotenoids and tocopherols in marine microalgae, Nannochloropsis sp. and Chaetoceros sp. Malays J Nutr 15:77–86PubMedGoogle Scholar
  25. Guedes AC, Amaro HM, Malcata FX (2011) Microalgae as sources of carotenoids. Mar Drugs 9:625–644CrossRefPubMedPubMedCentralGoogle Scholar
  26. Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28:977–982CrossRefPubMedGoogle Scholar
  27. Jang YS, Lee J, Malaviya A, do Seung Y, Cho JH, Lee SY (2012a) Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering. Biotechnol J 7:186–198CrossRefPubMedGoogle Scholar
  28. Jang YS, Park JM, Choi S, Choi YJ, Seung DY, Cho JH, Lee SY (2012b) Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches. Biotechnol Adv 30:989–1000CrossRefPubMedGoogle Scholar
  29. Kim HU, Kim TY, Lee SY (2008) Metabolic flux analysis and metabolic engineering of microorganisms. Mol Biosyst 4:113–120CrossRefPubMedGoogle Scholar
  30. Kohlstedt M, Becker J, Wittmann C (2010) Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism. Appl Microbiol Biotechnol 88:1065–1075CrossRefPubMedGoogle Scholar
  31. Kruse O, Rupprecht J, Bader KP, Thomas-Hall S, Schenk PM, Finazzi G, Hankamer B (2005) Improved photobiological H2 production in engineered green algal cells. J Biol Chem 280:34170–34177CrossRefPubMedGoogle Scholar
  32. Lee SY (2010a) Systems metabolic engineering for chemicals and materials. J Biotechnol 150:S1CrossRefGoogle Scholar
  33. Lee SY (2010b) Systems metabolic engineering for chemicals and materials. J Biotechnol 150:S574CrossRefGoogle Scholar
  34. Lee SY, Park JH (2010) Integration of systems biology with bioprocess engineering: L-threonine production by systems metabolic engineering of Escherichia coli. Adv Biochem Eng Biotechnol 120:1–19CrossRefPubMedGoogle Scholar
  35. Lee JM, Gianchandani EP, Papin JA (2006) Flux balance analysis in the era of metabolomics. Brief Bioinform 7:140–150CrossRefPubMedGoogle Scholar
  36. Lee JW, Kim TY, Jang YS, Choi S, Lee SY (2011) Systems metabolic engineering for chemicals and materials. Trends Biotechnol 29:370–378CrossRefPubMedGoogle Scholar
  37. Macias-Sanchez MD, Mantell Serrano C, Rodriguez Rodriguez M, Martinez de la Ossa E, Lubian LM, Montero O (2008) Extraction of carotenoids and chlorophyll from microalgae with supercritical carbon dioxide and ethanol as cosolvent. J Sep Sci 31:1352–1362CrossRefPubMedGoogle Scholar
  38. Melis A, Seibert M, Ghirardi ML (2007) Hydrogen fuel production by transgenic microalgae. Adv Exp Med Biol 616:110–121CrossRefPubMedGoogle Scholar
  39. Mendoza E (2007) What we can learn from a genome scale model of unicellular metabolism? Amino Acids 33(3):XXVGoogle Scholar
  40. Mo ML, Jamshidi N, Palsson BO (2007) A genome-scale, constraint-based approach to systems biology of human metabolism. Mol Biosyst 3:598–603CrossRefPubMedGoogle Scholar
  41. Moroney JV, Wilson BJ, Tolbert NE (1986) Glycolate metabolism and excretion by Chlamydomonas reinhardtii. Plant Physiol 82:821–826CrossRefPubMedPubMedCentralGoogle Scholar
  42. Oberhardt MA, Palsson BO, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320CrossRefPubMedPubMedCentralGoogle Scholar
  43. Orth JD, Thiele I, Palsson BO (2010) What is flux balance analysis? Nat Biotechnol 28:245–248CrossRefPubMedPubMedCentralGoogle Scholar
  44. Park JM, Kim TY, Lee SY (2009) Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv 27:979–988CrossRefPubMedGoogle Scholar
  45. Potvin G, Zhang Z (2010) Strategies for high-level recombinant protein expression in transgenic microalgae: a review. Biotechnol Adv 28:910–918CrossRefPubMedGoogle Scholar
  46. Quek L, Nielsen LK (2008) On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Inform 21:89–100PubMedGoogle Scholar
  47. Rudd KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60–64CrossRefPubMedPubMedCentralGoogle Scholar
  48. Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6:1290–1307CrossRefPubMedPubMedCentralGoogle Scholar
  49. Schwartz JM, Gaugain C, Nacher JC, de Daruvar A, Kanehisa M (2007) Observing metabolic functions at the genome scale. Genome Biol 8(6):R123CrossRefPubMedPubMedCentralGoogle Scholar
  50. Spencer KG, Togasaki RK (1981) Limitations on the utilization of glycolate by Chlamydomonas reinhardtii. Plant Physiol 68:28–32CrossRefPubMedPubMedCentralGoogle Scholar
  51. Stabenau H, Winkler U (2005) Glycolate metabolism in green algae. Physiol Plant 123:235–245CrossRefGoogle Scholar
  52. Thiele I, Palsson BO (2010a) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121CrossRefPubMedPubMedCentralGoogle Scholar
  53. Thiele I, Palsson BO (2010b) Reconstruction annotation jamborees: a community approach to systems biology. Mol Syst Biol 6:361CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Cristiana G. O. Dal’Molin
    • 1
  • Lars K. Nielsen
    • 1
  1. 1.Australian Institute for Bioengineering and Nanotechnology (AIBN)The University of QueenslandBrisbaneAustralia

Personalised recommendations