Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

BMC Syst Biol. 2017 Jul 4;11(1):66. doi: 10.1186/s12918-017-0441-1.


Background: Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high capacity to produce polyunsaturated fatty acids and triacylglycerols. It has been used as a source of biofuel, pigments and food supplements, like Omega 3. Only some Nannochloropsis species have been sequenced, but none of them benefit from a genome-scale metabolic model (GSMM), able to predict its metabolic capabilities.

Results: We present iNS934, the first GSMM for N. salina, including 2345 reactions, 934 genes and an exhaustive description of lipid and nitrogen metabolism. iNS934 has a 90% of accuracy when making simple growth/no-growth predictions and has a 15% error rate in predicting growth rates in different experimental conditions. Moreover, iNS934 allowed us to propose 82 different knockout strategies for strain optimization of triacylglycerols.

Conclusions: iNS934 provides a powerful tool for metabolic improvement, allowing predictions and simulations of N. salina metabolism under different media and genetic conditions. It also provides a systemic view of N. salina metabolism, potentially guiding research and providing context to -omics data.

Keywords: Genome-scale Metabolic model; Microalgæ; Nannochloropsis salina; TAG.

MeSH terms

  • Chromosome Mapping
  • Gene Expression Profiling
  • Genetic Engineering
  • Genomics*
  • Lipids / biosynthesis*
  • Microalgae / genetics*
  • Microalgae / metabolism*
  • Models, Biological*
  • Molecular Sequence Annotation
  • Nitrogen / metabolism
  • Stramenopiles / genetics*
  • Stramenopiles / metabolism*


  • Lipids
  • Nitrogen