Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production

Abstract

The aim of this study was to reconstruct protein-protein interaction map to allow researcher to identify pathway, biological roles and dynamic assembly of microalgae network pathways contributing to lipid production. The constructed PPI network was then characterised, and potential modifications were proposed based on this network to improve lipid production for mass biodiesel production. This bioinformatic approach is used to avoid the time consuming and expensive modification using high throughput approaches. In this study, literature search and data mining of rich information were interpreted into visualized outputs using Cystoscape. The outputs were then integrated and analysed to provide meaningful and reliable data. The study found that the constructed network consists of 153 nodes (proteins) and 1073 edges (interaction between proteins) with node degree R2 coefficient distribution of 0.193 to exponent -0.387 denoting that the protein distributes randomly in the network and has clustering coefficient of 0.641 which was characterised by a highly connected node. The acyl-lipid (7-3)-desaturase (EDP09855) was identified as a bottleneck protein and a putative perturbation target for high quality biodiesel production. Cytoscape simulation and integration showed that alkaline growth conditions and phosphate and iron supplementation influenced PPI-directed pathway of Chlamydomonas sp. (model species) to glycerol lipid metabolism and fatty acid biosynthesis important for achieving high lipid productivity. In actual experimentation, microalgae Nannochloropsis oculata achieved highest percent of lipid yield when cultured in pH 8 growth conditions (3.45 %) or when growth was supplemented with 0.1 g/L phosphate (5.70 %) and 9.44 mg/L iron (6.21 %). Even though Cytoscape integration of three different vitamin B supplementation showed only minor possibility of pathway direction towards fatty acid biosynthesis in model species, maximum lipid productivity was achieved for N. oculata cultured using 500 µg/L biotin (4.98%), 50 µg/L thiamine (4.82%) and 0.5 µg/L cobalamin (7.59%). Altogether, computational biological pathway reconstruction positively supported network perturbations to optimize microalgae lipid productivity and actual experimentation validated the protein-protein network.