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Microbiology and Biotechnology Letters

Research Article(보문)

Microbial Biotechnology  |  Synthetic Biology and Metabolic Engineering

Microbiol. Biotechnol. Lett.

Received: September 22, 2023; Revised: September 27, 2023

A Novel Draft Genome-scale Reconstruction Model of Isochrysis sp: Exploring Metabolic Pathways for Sustainable Aquaculture Innovations

Abhishek Sengupta 1, Tushar Gupta 1, Aman Chakraborty 1, Sudeepti Kulshrestha 1, Ritu Redhu 1, Raya Bhattacharya 2, Archana Tiwari 2 and Priyanka Narad 1*

1Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh- 201301, India, 2Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh-201301, India

Correspondence to :
Priyanka Narad, Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh- 201301, India [201301]
Fax : +919999302904, E-mail : priyanka.narad@gmail.com

Abstract

Isochrysis sp. is a sea microalga that has become a species of interest because of the extreme lipid content and rapid growth rate of this organism indicating its potential for efficient bio-fuel production. Using genome sequencing/genome-scale modeling for the prediction of Isochrysis sp. metabolic utilities there is high scope for the identification of essential pathways for the extraction of byproducts of interest at a higher rate. In our work, we design and pre-sent iIsochr964, a genome-scale metabolic model of Isochrysis sp. including 4315 reactions, 934 genes, and 1879 metabolites, which are distributed among fourteen compartments. For model validation, experimental culture, and isolation of Isochrysis sp. were performed and biomass values were used for validation of the genome-scale model. OptFlux was instrumental in uncovering several novel metabolites that influence the organism's metabolism by in-creasing the flux of interacting metabolites, such as Malonyl-CoA, EPA, Protein and others. iIsochr964 provides a compelling resource of metabolic understanding to revolutionize its industrial applications, thereby fostering sustainable development and allowing estimations and simulations of the organism metabolism under varying physiological, chemical, and genetic conditions. It is also useful in principle to provide a systemic view of Isochrysis sp. metabolism, efficiently guiding research and granting context to omics data.

Keywords: Genome-scale Metabolic model, Isochrysis, Flux balance analysis, metabolic engineering, Aquaculture, COBRA Toolbox

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