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

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 wer...

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Main Author:	Mahat, Katijah
Format:	Thesis
Language:	English
Published:	2019
Subjects:	TP Chemical technology
Online Access:	http://eprints.utm.my/id/eprint/81055/1/KatijahMahatPFS2019.pdf
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spelling	my-utm-ep.810552019-07-24T03:06:35Z Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production 2019-01 Mahat, Katijah TP Chemical technology 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. 2019-01 Thesis http://eprints.utm.my/id/eprint/81055/ http://eprints.utm.my/id/eprint/81055/1/KatijahMahatPFS2019.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:125079 phd doctoral Universiti Teknologi Malaysia, Faculty of Science Faculty of Science
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	TP Chemical technology
spellingShingle	TP Chemical technology Mahat, Katijah Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
description	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.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Mahat, Katijah
author_facet	Mahat, Katijah
author_sort	Mahat, Katijah
title	Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
title_short	Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
title_full	Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
title_fullStr	Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
title_full_unstemmed	Reconstruction of Nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
title_sort	reconstruction of nannochloropsis oculata protein-protein interaction network for growth and triacylglycerol production
granting_institution	Universiti Teknologi Malaysia, Faculty of Science
granting_department	Faculty of Science
publishDate	2019
url	http://eprints.utm.my/id/eprint/81055/1/KatijahMahatPFS2019.pdf
_version_	1747818300292726784

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

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