Microbiology and Biotechnology Letters (한국미생물·생명공학회지)

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

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

  • Abhishek Sengupta (Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University) ;
  • Tushar Gupta (Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University) ;
  • Aman Chakraborty (Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University) ;
  • Sudeepti Kulshrestha (Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University) ;
  • Ritu Redhu (Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University) ;
  • Raya Bhattacharjya (Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University) ;
  • Archana Tiwari (Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University) ;
  • Priyanka Narad (Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University)
  • Received : 2023.09.22
  • Accepted : 2023.10.08
  • Published : 2024.06.28
Download PDF
⟨ Previous Next ⟩

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 biofuel 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 present 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 increasing 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

Acknowledgement

We would like to acknowledge Dr. Ashok K. Chauhan, Founder President, Amity University Uttar Pradesh for providing us the opportunity to conduct research. We would also like thank Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University for providing us necessary resources.

References

  1. Matos J, Cardoso C, Gomes A, Campos AM, Fal P, Afonso C, et al. 2019. Bioprospection of Isochrysis galbana and its potential as a nutraceutical. Food Funct. 10: 7333-7342.
  2. Bonfanti C, Cardoso C, Afonso C, Matos J, Garcia T, Tanni S, et al. 2018. Potential of microalga Isochrysis galbana: Bioactivity and bioaccessibility. Algal Res. 29: 242-248.
  3. Cao J-Y, Kong Z-Y, Ye M-W, Ling T, Chen K, Xu J-L, et al. 2020. Comprehensive comparable study of metabolomic and transcriptomic profiling of Isochrysis galbana exposed to high temperature, an important diet microalgal species. Aquaculture 521: 735034.
  4. Passi A, Tibocha-Bonilla JD, Kumar M, Tec-Campos D, Zengler K, Zuniga C. 2021. Genome-scale metabolic modeling enables in-depth understanding of big data. Metabolites 12: 14.
  5. Gupta T, Vashistha S, Kulshrestha S, Narad P, Sengupta A. 2023. Mucormycosis metabolic network modeling: A constraint-based approach. 2023 6th International Conference on Information Systems and Computer Networks (ISCON).
  6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
  7. Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. 2022. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51: D587-D592.
  8. Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, et al. 2017. The BioCyc collection of microbial genomes and metabolic pathways. Brief. Bioinform. 20: 1085-1093.
  9. Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, et al. 2019. The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Res. 48: D445-D453.
  10. Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, et al. 2021. Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 50: D693-D700.
  11. Bhattacharjya R, Singh PK, Mishra B, Saxena A, Tiwari A. 2021. Phycoprospecting the nutraceutical potential of Isochrysis sp. as a source of aquafeed and other high-value products. Aquac. Res. 52: 2988-2995.
  12. Guillard RRL, Ryther JH. 1962. Studies of marine planktonic diatoms: Cyclotella nana hustedt, and Ddetonula confervacea (cleve) gran. Canadian J. Microbiol. 8: 229-239.
  13. Andersen RA, Kawachi M. 2005. Traditional microalgae isolation techniques. Algal culturing techniques (pp. 83-100). Elsevier Academic Press.
  14. Kim SM, Kang S-W, Kwon O-N, Chung D, Pan C-H. 2012. Fucoxanthin as a major carotenoid in Isochrysis aff. galbana: Characterization of extraction for commercial application. J. Korean Soc. Appl. Biol. Chem. 55: 477-483.
  15. Bhattacharjya R, Kiran Marella T, Tiwari A, Saxena A, Kumar Singh P, Mishra B. 2020. Bioprospecting of marine diatoms Thalassiosira, Skeletonema and Chaetoceros for lipids and other value-added products. Bioresour. Technol. 318: 124073.
  16. Bligh EG, Dyer WJ. 1959. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37: 911-917.
  17. Wang X-W, Huang L, Ji P-Y, Chen C-P, Li X-S, Gao Y-H, et al. 2019. Using a mixture of wastewater and seawater as the growth medium for wastewater treatment and lipid production by the marine diatom Phaeodactylum tricornutum. Bioresour. Technol. 289: 121681.
  18. Kumar Singh P, Bhattacharjya R, Mishra B, Saxena A, Tiwari A. 2022. A multifaceted approach towards valorizing diatom Thalassiosira weissflogii, cultivated on diluted municipal wastewater for enhanced biodiesel production. Fuel 328: 125311.
  19. Sarwer A, Hamed SM, Osman AI, Jamil F, Al-Muhtaseb AH, Alhajeri NS, et al. 2022. Algal biomass valorization for biofuel production and carbon sequestration: a review. Environ. Chem. Lett. 20: 2797-2851.
  20. Nagappan S, Das P, AbdulQuadir M, Thaher M, Khan S, Mahata C, et al. 2021. Potential of microalgae as a sustainable feed ingredient for aquaculture. J. Biotechnol. 341: 1-20.
  21. Narad P, Kulshrestha S, Chikara A, Gupta V, Kakrania M, Saxena R, et al. 2023. Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets. J. Biomol. Struct. Dyn. 2023: 1-16.
  22. Bharti S, Sengupta A, Chugh P, Narad P. PluriMetNet: 2022. A dynamic electronic model decrypting the metabolic variations in human embryonic stem cells (hESCs) at fluctuating oxygen concentrations. J. Biomol. Struct. Dyn. 40: 4570-4578.