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Robainas-Del-Pino Y, Viader-Salvadó JM, Herrera-Estala AL, Guerrero-Olazarán M. Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator. World J Microbiol Biotechnol 2023; 39:246. [PMID: 37420160 DOI: 10.1007/s11274-023-03682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris) is a widely used host for extracellularly producing heterologous proteins via an expression cassette integrated into the yeast genome. A strong promoter in the expression cassette is not always the most favorable choice for heterologous protein production, especially if the correct folding of the protein and/or post-translational processing is the limiting step. The transcriptional terminator is another regulatory element in the expression cassette that can modify the expression levels of the heterologous gene. In this work, we identified and functionally characterized the promoter (P1033) and transcriptional terminator (T1033) of a constitutive gene (i.e., the 1033 gene) with a weak non-methanol-dependent transcriptional activity. We constructed two K. phaffii strains with two combinations of the regulatory DNA elements from the 1033 and AOX1 genes (i.e., P1033-TAOX1 and P1033-T1033 pairs) and evaluated the impact of the regulatory element combinations on the transcript levels of the heterologous gene and endogenous 1033 and GAPDH genes in cells grown in glucose or glycerol, and on the extracellular product/biomass yield. The results indicate that the P1033 has a 2-3% transcriptional activity of the GAP promoter and it is tunable by cell growth and the carbon source. The combinations of the regulatory elements rendered different transcriptional activity of the heterologous and endogenous genes that were dependent on the carbon source. The promoter-terminator pair and the carbon source affected the heterologous gene translation and/or protein secretion pathway. Moreover, low heterologous gene-transcript levels along with glycerol cultures increased translation and/or protein secretion.
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Affiliation(s)
- Yanelis Robainas-Del-Pino
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - José María Viader-Salvadó
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| | - Ana Lucía Herrera-Estala
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Guerrero-Olazarán
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
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Biko OD, Viljoen-Bloom M, van Zyl WH. Medium optimization for enhanced production of recombinant lignin peroxidase in Pichia pastoris. Biotechnol Lett 2023; 45:105-113. [PMID: 36400875 DOI: 10.1007/s10529-022-03321-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Different cultivation conditions and parameters were evaluated to improve the production and secretion of a recombinant Phanerochaete chrysosporium lipH8 gene in Komagataella phaffii (Pichia pastoris). RESULTS The recombinant lipH8 gene with its native secretion signal was successfully cloned and expressed in Komagataella phaffii (Pichia pastoris) under the control of the alcohol oxidase 1 promoter (PAOX1). The results revealed that co-feeding with sorbitol and methanol increased rLiP secretion by 5.9-fold compared to the control conditions. The addition of 1 mM FeSO4 increased LiP activity a further 6.0-fold during the induction phase. Moreover, the combination of several optimal conditions and parameters yielded an extracellular rLiP activity of 20.05 U l-1, which is more than ten-fold higher relative to standard growth conditions (BMM10 medium, pH 6 and 30 °C). CONCLUSION Extracellular activity of a recombinant LiP expressed in P. pastoris increased more than ten-fold when co-feeding sorbitol and methanol as carbon sources, together with urea as nitrogen source, FeSO4 supplementation, lower pH and lower cultivation temperature.
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Affiliation(s)
- Odwa D Biko
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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Ergün BG, Laçın K, Çaloğlu B, Binay B. Second generation Pichia pastoris strain and bioprocess designs. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:150. [PMID: 36581872 PMCID: PMC9798597 DOI: 10.1186/s13068-022-02234-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/04/2022] [Indexed: 12/30/2022]
Abstract
Yeast was the first microorganism used by mankind for biotransformation processes that laid the foundations of industrial biotechnology. In the last decade, Pichia pastoris has become the leading eukaryotic host organism for bioproduct generation. Most of the P. pastoris bioprocess operations has been relying on toxic methanol and glucose feed. In the actual bioeconomy era, for sustainable value-added bioproduct generation, non-conventional yeast P. pastoris bioprocess operations should be extended to low-cost and renewable substrates for large volume bio-based commodity productions. In this review, we evaluated the potential of P. pastoris for the establishment of circular bioeconomy due to its potential to generate industrially relevant bioproducts from renewable sources and waste streams in a cost-effective and environmentally friendly manner. Furthermore, we discussed challenges with the second generation P. pastoris platforms and propose novel insights for future perspectives. In this regard, potential of low cost substrate candidates, i.e., lignocellulosic biomass components, cereal by-products, sugar industry by-products molasses and sugarcane bagasse, high fructose syrup by-products, biodiesel industry by-product crude glycerol, kitchen waste and other agri-food industry by products were evaluated for P. pastoris cell growth promoting effects and recombinant protein production. Further metabolic pathway engineering of P. pastoris to construct renewable and low cost substrate utilization pathways was discussed. Although, second generation P. pastoris bioprocess operations for valorisation of wastes and by-products still in its infancy, rapidly emerging synthetic biology tools and metabolic engineering of P. pastoris will pave the way for more sustainable environment and bioeconomy. From environmental point of view, second generation bioprocess development is also important for waste recycling otherwise disposal of carbon-rich effluents creates environmental concerns. P. pastoris high tolerance to toxic contaminants found in lignocellulosic biomass hydrolysate and industrial waste effluent crude glycerol provides the yeast with advantages to extend its applications toward second generation P. pastoris strain design and bioprocess engineering, in the years to come.
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Affiliation(s)
- Burcu Gündüz Ergün
- grid.18376.3b0000 0001 0723 2427National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey ,Biotechnology Research Center, Ministry of Agriculture and Forestry, 06330 Ankara, Turkey
| | - Kübra Laçın
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Buse Çaloğlu
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Barış Binay
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey ,grid.448834.70000 0004 0595 7127BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400 Gebze Kocaeli, Turkey
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Characterization of highly gelatinous patatin storage protein from Pichia pastoris. Food Res Int 2022; 162:111925. [DOI: 10.1016/j.foodres.2022.111925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022]
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Erden-Karaoğlan F, Karaoğlan M. Applicability of the heterologous yeast promoters for recombinant protein production in Pichia pastoris. Appl Microbiol Biotechnol 2022; 106:7073-7083. [PMID: 36163554 DOI: 10.1007/s00253-022-12183-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/05/2022] [Accepted: 09/11/2022] [Indexed: 11/02/2022]
Abstract
Promoter choice is an important step in recombinant protein production, which directly determines the expression manner as constitutive or inducible and the expression level of the recombinant protein. This study aims to investigate the applicability of heterologous yeast promoters (Kluyveromyces marxianus TPI, Hansenula polymorpha PMA, Candida tropicalis ICL, and Saccharomyces cerevisiae CUP) in Pichia pastoris. The regulation mode of the CtICL and ScCUP promoters in P. pastoris was found to be inducible and that of the KmTPI and HpPMA was constitutive. The carbon sources in which the promoters exhibited the highest activity were determined as glycerol for PMA and TPI, glucose for CUP, and ethanol for ICL. The DNA region showing the highest activity was determined as 1000 bp for all promoters by promoter deletion analysis. Results from the study demonstrate the potential of inducible and constitutive heterologous promoters allowing expression under different conditions in the P. pastoris expression system and offers alternatives to frequently used promoters. KEY POINTS: • Heterologous promoters exhibited similar expression pattern in P. pastoris with its native host. • HpPMA has the highest promoter activity among the heterologous promoters tested. • Reporter gene expression with ScCUP is responsive to elevating Cu2+in P. pastoris.
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Affiliation(s)
- Fidan Erden-Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye.
| | - Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye
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Haghighi Poodeh S, Ranaei Siadat SO, Arjmand S, Khalifeh Soltani M. Improving AOX1 promoter efficiency by overexpression of Mit1 transcription factor. Mol Biol Rep 2022; 49:9379-9386. [PMID: 36002652 DOI: 10.1007/s11033-022-07790-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/12/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Reprogramming in transcriptional regulation provides an effective tool for adjusting cellular metabolic activities. The strong methanol-inducible alcohol oxidase-1 promoter (pAOX1) is commonly used for heterologous gene expression in the yeast Pichia pastoris. Here, we present a novel Pichia pastoris strain engineered to co-express methanol-induced transcription factor 1 (Mit1) and the target protein. Mit1 upregulates pAOX1 in response to methanol. METHODS AND RESULTS Two model proteins (VEGF and eGFP) have been used as the target proteins under the control of pAOX1. The sequence of Mit1 had obtained from the yeast genome and likewise cloned under the control of pAOX1. The results indicated a 1.9 and 2.2 fold increase in the detected VEGF and eGFP, respectively, when co-expressed with Mit1. Furthermore, the double-recombinant cells, containing Mit-1 and eGFP, produced 1.3 fold more eGFP when the methanol feeding concentration was doubled. The real-time PCR indicated a slight increase in the Mit1 expression, probably due to the negative regulatory feedback loop that exists for the intrinsic yeast Mit1. Overexpression of Mit1 also led to duplication of AOX1 enzyme activity, which may enhance the yeast cells' capacity for methanol detoxification. CONCLUSION Overexpression of Mit1 could be considered a promising strategy for upregulation of target recombinant proteins in Pichia pastoris. Intracellular overexpression of Mit1 upregulates the heterologous target gene (eGFP) production, which is expressed under the control of pAOX1.
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Affiliation(s)
- Samin Haghighi Poodeh
- Protein Research Center, Shahid Beheshti University, P.O. Box: 19839, 69411, Tehran, Iran
| | | | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, P.O. Box: 19839, 69411, Tehran, Iran.
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de Sá Magalhães S, Keshavarz-Moore E. Pichia pastoris ( Komagataella phaffii) as a Cost-Effective Tool for Vaccine Production for Low- and Middle-Income Countries (LMICs). Bioengineering (Basel) 2021; 8:119. [PMID: 34562941 PMCID: PMC8468848 DOI: 10.3390/bioengineering8090119] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/05/2021] [Accepted: 08/24/2021] [Indexed: 01/26/2023] Open
Abstract
Vaccination is of paramount importance to global health. With the advent of the more recent pandemics, the urgency to expand the range has become even more evident. However, the potential limited availability and affordability of vaccines to resource low- and middle-income countries has created a need for solutions that will ensure cost-effective vaccine production methods for these countries. Pichia pastoris (P. pastoris) (also known as Komagataella phaffii) is one of the most promising candidates for expression of heterologous proteins in vaccines development. It combines the speed and ease of highly efficient prokaryotic platforms with some key capabilities of mammalian systems, potentially reducing manufacturing costs. This review will examine the latest developments in P. pastoris from cell engineering and design to industrial production systems with focus on vaccine development and with reference to specific key case studies.
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Affiliation(s)
| | - Eli Keshavarz-Moore
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK;
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Püllmann P, Weissenborn MJ. Improving the Heterologous Production of Fungal Peroxygenases through an Episomal Pichia pastoris Promoter and Signal Peptide Shuffling System. ACS Synth Biol 2021; 10:1360-1372. [PMID: 34075757 DOI: 10.1021/acssynbio.0c00641] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fungal peroxygenases (UPOs) have emerged as oxyfunctionalization catalysts of tremendous interest in recent years. However, their widespread use in the field of biocatalysis is still hampered by their challenging heterologous production, substantially limiting the panel of accessible enzymes for investigation and enzyme engineering. Building upon previous work on UPO production in yeast, we have developed a combined promoter and signal peptide shuffling system for episomal high throughput UPO production in the industrially relevant, methylotrophic yeast Pichia pastoris. Eleven endogenous and orthologous promoters were shuffled with a diverse set of 17 signal peptides. Three previously described UPOs were selected as first test set, leading to the identification of beneficial promoter/signal peptide combinations for protein production. We applied the system then successfully to produce two novel UPOs: MfeUPO from Myceliophthora fergusii and MhiUPO from Myceliophthora hinnulea. To demonstrate the feasibility of the developed system to other enzyme classes, it was applied for the industrially relevant lipase CalB and the laccase Mrl2. In total, approximately 3200 transformants of eight diverse enzymes were screened and the best promoter/signal peptide combinations studied at various cofeeding, derepression, and induction conditions. High volumetric production titers were achieved by subsequent creation of stable integration lines and harnessing orthologous promoters from Hansenula polymorpha. In most cases promising yields were also achieved without the addition of methanol under derepressed conditions. To foster the use of the episomal high throughput promoter/signal peptide Pichia pastoris system, we made all plasmids available through Addgene.
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Affiliation(s)
- Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 2, 06120 Halle (Saale), Germany
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Gao J, Jiang L, Lian J. Development of synthetic biology tools to engineer Pichia pastoris as a chassis for the production of natural products. Synth Syst Biotechnol 2021; 6:110-119. [PMID: 33997361 PMCID: PMC8113645 DOI: 10.1016/j.synbio.2021.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/13/2021] [Accepted: 04/26/2021] [Indexed: 01/12/2023] Open
Abstract
The methylotrophic yeast Pichia pastoris (a.k.a. Komagataella phaffii) is one of the most commonly used hosts for industrial production of recombinant proteins. As a non-conventional yeast, P. pastoris has unique biological characteristics and its expression system has been well developed. With the advances in synthetic biology, more efforts have been devoted to developing P. pastoris into a chassis for the production of various high-value compounds, such as natural products. This review begins with the introduction of synthetic biology tools for the engineering of P. pastoris, including vectors, promoters, and terminators for heterologous gene expression as well as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated System (CRISPR/Cas) for genome editing. This review is then followed by examples of the production of value-added natural products in metabolically engineered P. pastoris strains. Finally, challenges and outlooks in developing P. pastoris as a synthetic biology chassis are prospected.
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Affiliation(s)
- Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
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Established tools and emerging trends for the production of recombinant proteins and metabolites in Pichia pastoris. Essays Biochem 2021; 65:293-307. [PMID: 33956085 DOI: 10.1042/ebc20200138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/09/2021] [Accepted: 03/29/2021] [Indexed: 12/31/2022]
Abstract
Besides bakers' yeast, the methylotrophic yeast Komagataella phaffii (also known as Pichia pastoris) has been developed into the most popular yeast cell factory for the production of heterologous proteins. Strong promoters, stable genetic constructs and a growing collection of freely available strains, tools and protocols have boosted this development equally as thorough genetic and cell biological characterization. This review provides an overview of state-of-the-art tools and techniques for working with P. pastoris, as well as guidelines for the production of recombinant proteins with a focus on small-scale production for biochemical studies and protein characterization. The growing applications of P. pastoris for in vivo biotransformation and metabolic pathway engineering for the production of bulk and specialty chemicals are highlighted as well.
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Patra P, Das M, Kundu P, Ghosh A. Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 2021; 47:107695. [PMID: 33465474 DOI: 10.1016/j.biotechadv.2021.107695] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using 13C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.
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Affiliation(s)
- Pradipta Patra
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manali Das
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pritam Kundu
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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