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Pentjuss A, Bolmanis E, Suleiko A, Didrihsone E, Suleiko A, Dubencovs K, Liepins J, Kazaks A, Vanags J. Pichia pastoris growth-coupled heme biosynthesis analysis using metabolic modelling. Sci Rep 2023; 13:15816. [PMID: 37739976 PMCID: PMC10516909 DOI: 10.1038/s41598-023-42865-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023] Open
Abstract
Soy leghemoglobin is one of the most important and key ingredients in plant-based meat substitutes that can imitate the colour and flavour of the meat. To improve the high-yield production of leghemoglobin protein and its main component-heme in the yeast Pichia pastoris, glycerol and methanol cultivation conditions were studied. Additionally, in-silico metabolic modelling analysis of growth-coupled enzyme quantity, suggests metabolic gene up/down-regulation strategies for heme production. First, cultivations and metabolic modelling analysis of P. pastoris were performed on glycerol and methanol in different growth media. Glycerol cultivation uptake and production rates can be increased by 50% according to metabolic modelling results, but methanol cultivation-is near the theoretical maximum. Growth-coupled metabolic optimisation results revealed the best feasible upregulation (33 reactions) (1.47% of total reactions) and 66 downregulation/deletion (2.98% of total) reaction suggestions. Finally, we describe reaction regulation suggestions with the highest potential to increase heme production yields.
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Affiliation(s)
- Agris Pentjuss
- Microbiology and Biotechnology Institute, University of Latvia, Jelgavas Street 1, Riga, 1004, Latvia.
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia.
| | - Emils Bolmanis
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1 K-1, Riga, 1067, Latvia
| | - Anastasija Suleiko
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Elina Didrihsone
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Arturs Suleiko
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Konstantins Dubencovs
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Janis Liepins
- Microbiology and Biotechnology Institute, University of Latvia, Jelgavas Street 1, Riga, 1004, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1 K-1, Riga, 1067, Latvia
| | - Juris Vanags
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
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Sajid M, Stone SR, Kaur P. Phylogenetic Analysis and Protein Modelling of Isoflavonoid Synthase Highlights Key Catalytic Sites towards Realising New Bioengineering Endeavours. Bioengineering (Basel) 2022; 9:bioengineering9110609. [PMID: 36354520 PMCID: PMC9687675 DOI: 10.3390/bioengineering9110609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/01/2022] Open
Abstract
Isoflavonoid synthase (IFS) is a critical enzyme for the biosynthesis of over 2400 isoflavonoids. Isoflavonoids are an important class of plant secondary metabolites that have a range of pharmaceutical and nutraceutical properties. With growing interest in isoflavonoids from both research and industrial perspectives, efforts are being forwarded to enhance isoflavonoid production in-planta and ex-planta; therefore, in-silico analysis and characterisation of available IFS protein sequences are needed. The present study is the first-ever attempt toward phylogenetic analysis and protein modelling of available IFS protein sequences. Phylogenetic analysis has shown that IFS amino acid sequences have 86.4% pairwise identity and 26.5% identical sites, and the sequences were grouped into six different clades. The presence of a β-hairpin and extra loop at catalytic sites of Trifolium pratense, Beta vulgaris and Medicago truncatula, respectively, compared with Glycyrrhiza echinata are critical structural differences that may affect catalytic function. Protein docking highlighted the preference of selected IFS for liquiritigenin compared with naringenin and has listed T. pratense as the most efficient candidate for heterologous biosynthesis of isoflavonoids. The in-silico characterisation of IFS represented in this study is vital in realising the new bioengineering endeavours and will help in the characterisation and selection of IFS candidate enzymes for heterologous biosynthesis of isoflavonoids.
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