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Robertson NR, Trivedi V, Lupish B, Ramesh A, Aguilar Y, Carrera S, Lee S, Arteaga A, Nguyen A, Lenert-Mondou C, Harland-Dunaway M, Jinkerson R, Wheeldon I. Optimized genome-wide CRISPR screening enables rapid engineering of growth-based phenotypes in Yarrowia lipolytica. Metab Eng 2024:S1096-7176(24)00122-8. [PMID: 39278589 DOI: 10.1016/j.ymben.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/28/2024] [Accepted: 09/12/2024] [Indexed: 09/18/2024]
Abstract
CRISPR-Cas9 functional genomic screens uncover gene targets linked to various phenotypes for metabolic engineering with remarkable efficiency. However, these genome-wide screens face a number of design challenges, including variable guide RNA activity, ensuring sufficient genome coverage, and maintaining high transformation efficiencies to ensure full library representation. These challenges are prevalent in non-conventional yeast, many of which exhibit traits that are well suited to metabolic engineering and bioprocessing. To address these hurdles in the oleaginous yeast Yarrowia lipolytica, we designed a compact, high-activity genome-wide sgRNA library. The library was designed using DeepGuide, an sgRNA activity prediction algorithm and a large dataset of ∼50,000 sgRNAs with known activity. Three guides per gene enables redundant targeting of 98.8% of genes in the genome in a library of 23,900 sgRNAs. We deployed the optimized library to uncover genes essential to the tolerance of acetate, a promising alternative carbon source, and various hydrocarbons present in many waste streams. Our screens yielded several gene knockouts that improve acetate tolerance on their own and as double knockouts in media containing acetate as the sole carbon source. Analysis of the hydrocarbon screens revealed genes related to fatty acid and alkane metabolism in Y. lipolytica. The optimized CRISPR gRNA library and its successful use in Y. lipolytica led to the discovery of alternative carbon source-related genes and provides a workflow for creating high-activity, compact genome-wide libraries for strain engineering.
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Affiliation(s)
| | - Varun Trivedi
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Brian Lupish
- Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Adithya Ramesh
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Yuna Aguilar
- Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Stephanie Carrera
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Sangcheon Lee
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Anthony Arteaga
- Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA
| | - Alexander Nguyen
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | | | | | - Robert Jinkerson
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA; Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA.
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2
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Miranda SM, Belo I, Lopes M. Yarrowia lipolytica growth, lipids, and protease production in medium with higher alkanes and alkenes. World J Microbiol Biotechnol 2024; 40:318. [PMID: 39261393 PMCID: PMC11390925 DOI: 10.1007/s11274-024-04123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024]
Abstract
Two strains of Yarrowia lipolytica (CBS 2075 and DSM 8218) were first studied in bioreactor batch cultures, under different controlled dissolved oxygen concentrations (DOC), to assess their ability to assimilate aliphatic hydrocarbons (HC) as a carbon source in a mixture containing 2 g·L-1 of each alkane (dodecane and hexadecane), and 2 g·L-1 hexadecene. Both strains grew in the HC mixture without a lag phase, and for both strains, 30 % DOC was sufficient to reach the maximum values of biomass and lipids. To enhance lipid-rich biomass and enzyme production, a pulse fed-batch strategy was tested, for the first time, with the addition of one or three pulses of concentrated HC medium. The addition of three pulses of the HC mixture (total of 24 g·L-1 HC) did not hinder cell proliferation, and high protease (> 3000 U·L-1) and lipids concentrations of 3.4 g·L-1 and 4.3 g·L-1 were achieved in Y. lipolytica CBS 2075 and DSM 8218 cultures, respectively. Lipids from the CBS 2075 strain are rich in C16:0 and C18:1, resembling the composition of palm oil, considered suitable for the biodiesel industry. Lipids from the DSM 8218 strain were predominantly composed of C16:0 and C16:1, the latter being a valuable monounsaturated fatty acid used in the pharmaceutical industry. Y. lipolytica cells exhibited high intrinsic surface hydrophobicity (> 69 %), which increased in the presence of HC. A reduction in surface tension was observed in both Y. lipolytica cultures, suggesting the production of extracellular biosurfactants, even at low amounts. This study marks a significant advancement in the valorization of HC for producing high-value products by exploring the hydrophobic compounds metabolism of Y. lipolytica.
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Affiliation(s)
- Sílvia M Miranda
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Belo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Marlene Lopes
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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3
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Yang H, Guo J, Zhang L, Shen W, Xia Y, Chen X. Systematic metabolic engineering for improved synthesis of perillic acid in Candida tropicalis. Appl Microbiol Biotechnol 2024; 108:447. [PMID: 39190181 DOI: 10.1007/s00253-024-13279-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 08/28/2024]
Abstract
Perillic acid has been studied as an anticancer and antimicrobial drug. Production of perillic acid has attracted considerable attention. Meanwhile, Candida tropicalis is an unconventional diploid yeast, most significantly characterized by its ability to metabolize alkanes or fatty acids for growth and proliferation. Therefore, perillic acid's precursor (L-limonene) in C. tropicalis was firstly synthesized by expressing a Mentha spicata L-limonene synthase gene, LS_Ms in this work. Expression of a gene which encoded for a truncated version of tLS_Ms increased the production of L-limonene with a 2.78-fold increase in the titer over C. tropicalis GJR-LS-01. Compartmentalized expression of the gene tLS_Ms inhibited the production of L-limonene in C. tropicalis compared to cytoplasmic expression. Cytoplasmic overexpression of seven precursor synthesis genes significantly enhanced the production of L-limonene in C. tropicalis compared to their compartmentalized expression (mitochondria or peroxisomes), which increased by 31.7-fold in C. tropicalis GJR-tLS-01. The L-limonene titer in C. tropicalis GJR-EW-tLS-04 overexpressing the mutant gene ERG20WW in the cytoplasm was significantly increased, 11.33-fold higher than the control. The titer of L-limonene for 60 g/L glucose was increased by 1.40-fold compared to the control. Finally, a Salvia miltiorrhiza cytochrome P450 enzyme gene CYP7176 and an Arabidopsis thaliana NADPH cytochrome P450 reductase gene CPR were heterologously expressed in C. tropicalis GJR-EW-tLS-04C for the synthesis of perillic acid, which reached a titer of 106.69 mg/L in a 5-L fermenter. This is the first report of de novo synthesis of perillic acid in engineered microorganisms. The results also showed that other chemicals may be efficiently produced in C. tropicalis. KEY POINTS: • Key genes cytoplasmic expression was conducive to L-limonene production in C. tropicalis. • Perillic acid was first synthesized de novo in engineered microorganisms. • The titer of perillic acid reached 106.69 mg/L in a 5-L fermenter.
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Affiliation(s)
- Haiquan Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jinrong Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Lihua Zhang
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Wei Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yuanyuan Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Kimura-Ishimaru C, Liang S, Matsuse K, Iwama R, Sato K, Watanabe N, Tezaki S, Horiuchi H, Fukuda R. Mar1, a high mobility group box protein, regulates n-alkane adsorption and cell morphology of the dimorphic yeast Yarrowia lipolytica. Appl Environ Microbiol 2024; 90:e0054624. [PMID: 39058021 PMCID: PMC11337826 DOI: 10.1128/aem.00546-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The dimorphic yeast Yarrowia lipolytica possesses an excellent ability to utilize n-alkane as a sole carbon and energy source. Although there are detailed studies on the enzymes that catalyze the reactions in the metabolic processes of n-alkane in Y. lipolytica, the molecular mechanism underlying the incorporation of n-alkane into the cells remains to be elucidated. Because Y. lipolytica adsorbs n-alkane, we postulated that Y. lipolytica incorporates n-alkane through direct interaction with it. We isolated and characterized mutants defective in adsorption to n-hexadecane. One of the mutants harbored a nonsense mutation in MAR1 (Morphology and n-alkane Adsorption Regulator 1) encoding a protein containing a high mobility group box. The deletion mutant of MAR1 exhibited defects in adsorption to n-hexadecane and filamentous growth on solid media, whereas the strain that overexpressed MAR1 exhibited hyperfilamentous growth. Fluorescence microscopic observations suggested that Mar1 localizes in the nucleus. RNA-sequencing analysis revealed the alteration of the transcript levels of several genes, including those encoding transcription factors and cell surface proteins, by the deletion of MAR1. These findings suggest that MAR1 is involved in the transcriptional regulation of the genes required for n-alkane adsorption and cell morphology transition.IMPORTANCEYarrowia lipolytica, a dimorphic yeast capable of assimilating n-alkane as a carbon and energy source, has been extensively studied as a promising host for bioconversion of n-alkane into useful chemicals and bioremediation of soil and water contaminated by petroleum. While the metabolic pathway of n-alkane in this yeast and the enzymes involved in this pathway have been well characterized, the molecular mechanism to incorporate n-alkane into the cells is yet to be fully understood. Due to the ability of Y. lipolytica to adsorb n-alkane, it has been hypothesized that Y. lipolytica incorporates n-alkane through direct interaction with it. In this study, we identified a gene, MAR1, which plays a crucial role in the transcriptional regulation of the genes necessary for the adsorption to n-alkane and the transition of the cell morphology in Y. lipolytica. Our findings provide valuable insights that could lead to advanced applications of Y. lipolytica in n-alkane bioconversion and bioremediation.
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Affiliation(s)
| | - Simiao Liang
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Katsuro Matsuse
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenta Sato
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Natsuhito Watanabe
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Tezaki
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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5
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Xu L, Bai X, Joong Oh E. Strategic approaches for designing yeast strains as protein secretion and display platforms. Crit Rev Biotechnol 2024:1-18. [PMID: 39138023 DOI: 10.1080/07388551.2024.2385996] [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: 04/02/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
Yeast has been established as a versatile platform for expressing functional molecules, owing to its well-characterized biology and extensive genetic modification tools. Compared to prokaryotic systems, yeast possesses advanced cellular mechanisms that ensure accurate protein folding and post-translational modifications. These capabilities are particularly advantageous for the expression of human-derived functional proteins. However, designing yeast strains as an expression platform for proteins requires the integration of molecular and cellular functions. By delving into the complexities of yeast-based expression systems, this review aims to empower researchers with the knowledge to fully exploit yeast as a functional platform to produce a diverse range of proteins. This review includes an exploration of the host strains, gene cassette structures, as well as considerations for maximizing the efficiency of the expression system. Through this in-depth analysis, the review anticipates stimulating further innovation in the field of yeast biotechnology and protein engineering.
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Affiliation(s)
- Luping Xu
- Department of Food Science, Purdue University, West Lafayette, IN, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
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6
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Escribano-Huesca A, Gila-Vilchez C, Amaro-da-Cruz A, Leon-Cecilla A, Palomo MG, Ortiz-Ruiz S, Ruiz FG, Moya-Ramirez I, Lopez-Lopez MT, Rodriguez-Arco L. Dynamically Reconfigurable Micro-Patterned Hydrogels Based on Magnetic Pickering Emulsion Droplets. Macromol Rapid Commun 2024:e2400242. [PMID: 39116442 DOI: 10.1002/marc.202400242] [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: 04/16/2024] [Revised: 07/06/2024] [Indexed: 08/10/2024]
Abstract
Reconfigurability within hydrogels has emerged as an attractive functionality that can be used in information encryption, cargo/delivery, environmental remediation, soft robotics, and medicine. Here micro-patterned polymer hydrogels capable of temperature-dependent reconfigurability are fabricated. For this, the hydrogels are provided with micron-sized Pickering emulsion droplets stabilized by magnetic particles, which are capable of harnessing energy from external force fields. The droplets can both migrate under magnetic field gradients and heat the environment when laser irradiated. These functions not only affect a single compartment but have higher-order effects on the mesoscale, thanks to the temperature-responsiveness of the polymeric network. This double responsiveness is exploited to control the spatial organization of hundreds of droplets within the hydrogel matrix and form predesigned and sophisticated patterns. Furthermore, pattern self-reconfiguration driven by the droplets themselves upon laser irradiation is induced. Finally, we show that due to their internal liquid phase, the droplets can be used as reservoirs of hydrophobic nutrients for living cells (i.e., Yarrowia lipolytica yeast) in the solid-like environment of the polymeric network, and demonstrate communication between the droplets and the cells to facilitate nutrient uptake. Altogether, the results provide opportunities for the development of stimuli-sensitive polymer hydrogels with post-synthesis reprogrammable response using micro-compartments as building blocks.
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Affiliation(s)
- Alfredo Escribano-Huesca
- Departamento de Física Aplicada, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, E-18014, Spain
| | - Cristina Gila-Vilchez
- Departamento de Física Aplicada, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, E-18014, Spain
| | - Alba Amaro-da-Cruz
- Departamento de Ingeniería Química, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
| | - Alberto Leon-Cecilla
- Departamento de Física Aplicada, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, E-18014, Spain
| | - Mikel G Palomo
- Departamento de Electrónica y Tecnología de Computadores, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
| | - Sergio Ortiz-Ruiz
- Departamento de Electrónica y Tecnología de Computadores, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
| | - Francisco G Ruiz
- Departamento de Electrónica y Tecnología de Computadores, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
| | - Ignacio Moya-Ramirez
- Departamento de Ingeniería Química, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
| | - Modesto T Lopez-Lopez
- Departamento de Física Aplicada, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, E-18014, Spain
| | - Laura Rodriguez-Arco
- Departamento de Física Aplicada, Campus de Fuentenueva, Universidad de Granada, Granada, E-18071, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, E-18014, Spain
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7
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Hassane AMA, Eldiehy KSH, Saha D, Mohamed H, Mosa MA, Abouelela ME, Abo-Dahab NF, El-Shanawany ARA. Oleaginous fungi: a promising source of biofuels and nutraceuticals with enhanced lipid production strategies. Arch Microbiol 2024; 206:338. [PMID: 38955856 DOI: 10.1007/s00203-024-04054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
Oleaginous fungi have attracted a great deal of interest for their potency to accumulate high amounts of lipids (more than 20% of biomass dry weight) and polyunsaturated fatty acids (PUFAs), which have a variety of industrial and biological applications. Lipids of plant and animal origin are related to some restrictions and thus lead to attention towards oleaginous microorganisms as reliable substitute resources. Lipids are traditionally biosynthesized intra-cellularly and involved in the building structure of a variety of cellular compartments. In oleaginous fungi, under certain conditions of elevated carbon ratio and decreased nitrogen in the growth medium, a change in metabolic pathway occurred by switching the whole central carbon metabolism to fatty acid anabolism, which subsequently resulted in high lipid accumulation. The present review illustrates the bio-lipid structure, fatty acid classes and biosynthesis within oleaginous fungi with certain key enzymes, and the advantages of oleaginous fungi over other lipid bio-sources. Qualitative and quantitative techniques for detecting the lipid accumulation capability of oleaginous microbes including visual, and analytical (convenient and non-convenient) were debated. Factors affecting lipid production, and different approaches followed to enhance the lipid content in oleaginous yeasts and fungi, including optimization, utilization of cost-effective wastes, co-culturing, as well as metabolic and genetic engineering, were discussed. A better understanding of the oleaginous fungi regarding screening, detection, and maximization of lipid content using different strategies could help to discover new potent oleaginous isolates, exploit and recycle low-cost wastes, and improve the efficiency of bio-lipids cumulation with biotechnological significance.
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Affiliation(s)
- Abdallah M A Hassane
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, P.O. Box 71524, Assiut, Egypt.
| | - Khalifa S H Eldiehy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, P.O. Box 71524, Assiut, Egypt
| | - Debanjan Saha
- Department of Molecular Biology and Biotechnology, Tezpur University, P.O. Box 784028, Assam, India
| | - Hassan Mohamed
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, P.O. Box 71524, Assiut, Egypt
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, P.O. Box 255000, Zibo, China
| | - Mohamed A Mosa
- Nanotechnology and Advanced Nano-Materials Laboratory (NANML), Plant Pathology Research Institute, Agricultural Research Center, P.O. Box 12619, Giza, Egypt
| | - Mohamed E Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, P.O. Box 11884, Cairo, Egypt
| | - Nageh F Abo-Dahab
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, P.O. Box 71524, Assiut, Egypt
| | - Abdel-Rehim A El-Shanawany
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, P.O. Box 71524, Assiut, Egypt
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8
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Poopanitpan N, Piampratom S, Viriyathanit P, Lertvatasilp T, Horiuchi H, Fukuda R, Kiatwuthinon P. SNF1 plays a crucial role in the utilization of n-alkane and transcriptional regulation of the genes involved in it in the yeast Yarrowia lipolytica. Heliyon 2024; 10:e32886. [PMID: 38975102 PMCID: PMC11226914 DOI: 10.1016/j.heliyon.2024.e32886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Yarrowia lipolytica is an ascomycetous yeast that can assimilate hydrophobic carbon sources including oil and n-alkane. The sucrose non-fermenting 1/AMP-activated protein kinase (Snf1/AMPK) complex is involved in the assimilation of non-fermentable carbon sources in various yeasts. However, the role of the Snf1/AMPK complex in n-alkane assimilation in Y. lipolytica has not yet been elucidated. This study aimed to clarify the role of Y. lipolytica SNF1 (YlSNF1) in the utilization of n-alkane. The deletion mutant of YlSNF1 (ΔYlsnf1) exhibited substantial growth defects on n-alkanes of various lengths (C10, C12, C14, and C16), and its growth was restored through the introduction of YlSNF1. Microscopic observations revealed that YlSnf1 tagged with enhanced green fluorescence protein showed dot-like distribution patterns in some cells cultured in the medium containing n-decane, which were not observed in cells cultured in the medium containing glucose or glycerol. The RNA sequencing analysis of ΔYlsnf1 cultured in the medium containing n-decane exhibited 302 downregulated and 131 upregulated genes compared with the wild-type strain cultured in the same medium. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that a significant fraction of the downregulated genes functioned in peroxisomes or were involved in the metabolism of n-alkane and fatty acids. Quantitative real-time PCR analysis confirmed the downregulation of 12 genes involved in the metabolism of n-alkane and fatty acid, ALK1-ALK3, ALK5, ADH7, PAT1, POT1, POX2, PEX3, PEX11, YAS1, and HFD3. Furthermore, ΔYlsnf1 exhibited growth defects on the medium containing the metabolites of n-alkane (fatty alcohol and fatty aldehyde). These findings suggest that YlSNF1 plays a crucial role in the utilization of n-alkane in Y. lipolytica. This study provides important insights into the advanced biotechnological applications of this yeast, including the bioconversion of n-alkane to useful chemicals and the bioremediation of petroleum-contaminated environments.
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Affiliation(s)
- Napapol Poopanitpan
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Program in Genetic Engineering, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Sorawit Piampratom
- Interdisciplinary Program in Genetic Engineering, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Patthanant Viriyathanit
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Threesara Lertvatasilp
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Pichamon Kiatwuthinon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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9
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Dickey RM, Gopal MR, Nain P, Kunjapur AM. Recent developments in enzymatic and microbial biosynthesis of flavor and fragrance molecules. J Biotechnol 2024; 389:43-60. [PMID: 38616038 DOI: 10.1016/j.jbiotec.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Flavors and fragrances are an important class of specialty chemicals for which interest in biomanufacturing has risen during recent years. These naturally occurring compounds are often amenable to biosynthesis using purified enzyme catalysts or metabolically engineered microbial cells in fermentation processes. In this review, we provide a brief overview of the categories of molecules that have received the greatest interest, both academically and industrially, by examining scholarly publications as well as patent literature. Overall, we seek to highlight innovations in the key reaction steps and microbial hosts used in flavor and fragrance manufacturing.
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Affiliation(s)
- Roman M Dickey
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Madan R Gopal
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Priyanka Nain
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA.
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10
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Loan T, Vickers CE, Ayliffe M, Luo M. β-Dicarbonyls Facilitate Engineered Microbial Bromoform Biosynthesis. ACS Synth Biol 2024; 13:1492-1497. [PMID: 38525720 PMCID: PMC11106770 DOI: 10.1021/acssynbio.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Ruminant livestock produce around 24% of global anthropogenic methane emissions. Methanogenesis in the animal rumen is significantly inhibited by bromoform, which is abundant in seaweeds of the genus Asparagopsis. This has prompted the development of livestock feed additives based on Asparagopsis to mitigate methane emissions, although this approach alone is unlikely to satisfy global demand. Here we engineer a non-native biosynthesis pathway to produce bromoform in vivo with yeast as an alternative biological source that may enable sustainable, scalable production of bromoform by fermentation. β-dicarbonyl compounds with low pKa values were identified as essential substrates for bromoform production and enabled bromoform synthesis in engineered Saccharomyces cerevisiae expressing a vanadate-dependent haloperoxidase gene. In addition to providing a potential route to the sustainable biological production of bromoform at scale, this work advances the development of novel microbial biosynthetic pathways for halogenation.
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Affiliation(s)
- Thomas
D. Loan
- CSIRO
Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
| | - Claudia E. Vickers
- ARC
Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre
of Agriculture and the Bioeconomy, School of Biology and Environmental
Science, Faculty of Science, Queensland
University of Technology, Brisbane, QLD 4000, Australia
| | - Michael Ayliffe
- CSIRO
Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
| | - Ming Luo
- CSIRO
Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
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11
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Bejenari M, Spedtsberg EML, Mathiesen J, Jeppesen AC, Cernat L, Toussaint A, Apostol C, Stoianov V, Pedersen TB, Nielsen MR, Sørensen JL. First-class - biosynthesis of 6-MSA and bostrycoidin type I polyketides in Yarrowia lipolytica. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1327777. [PMID: 38586602 PMCID: PMC10995274 DOI: 10.3389/ffunb.2024.1327777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 04/09/2024]
Abstract
Fungal polyketides are a large group of secondary metabolites, valuable due to their diverse spectrum of pharmacological activities. Polyketide biosynthesis in filamentous fungi presents some challenges: small yield and low-purity titers. To tackle these issues, we switched to the yeast Yarrowia lipolytica, an easily cultivable heterologous host. As an oleaginous yeast, Y. lipolytica displays a high flux of acetyl- and malonyl-CoA precursors used in lipid synthesis. Likewise, acetyl- and malonyl-CoA are the building blocks of many natural polyketides, and we explored the possibility of redirecting this flux toward polyketide production. Despite its promising prospect, Y. lipolytica has so far only been used for heterologous expression of simple type III polyketide synthases (PKSs) from plants. Therefore, we decided to evaluate the potential of Y. lipolytica by targeting the more complex fungal polyketides synthesized by type I PKSs. We employed a CRISPR-Cas9-mediated genome editing method to achieve markerless gene integration of the genes responsible for bostrycoidin biosynthesis in Fusarium solani (fsr1, fsr2, and fsr3) and 6-methylsalicylic acid (6-MSA) biosynthesis in Aspergillus hancockii (6MSAS). Moreover, we attempted titer optimization through metabolic engineering by overexpressing two enzymes, TGL4 and AOX2, involved in lipid β-oxidation, but we did not observe an effect on polyketide production. With maximum titers of 403 mg/L 6-MSA and 35 mg/L bostrycoidin, the latter being substantially higher than our previous results in Saccharomyces cerevisiae (2.2 mg/L), this work demonstrates the potential of Y. lipolytica as a platform for heterologous production of complex fungal polyketides.
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Affiliation(s)
- Mihaela Bejenari
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
- Department of Energy, Aalborg University, Esbjerg, Denmark
| | - Julie Mathiesen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Lucia Cernat
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Aouregane Toussaint
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire Végétale, CEA, CNRS, INRA, IRIG-LPCV, Grenoble, France
| | - Cristina Apostol
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Victor Stoianov
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
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12
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Sookai S, Akerman MP, Munro OQ. Chiral Au(III) chelates exhibit unique NCI-60 cytotoxicity profiles and interactions with human serum albumin. Dalton Trans 2024; 53:5089-5104. [PMID: 38375922 DOI: 10.1039/d3dt04024k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Au(III) bis(pyrrolide-imine) chelates are emerging as a class of versatile, efficacious metallodrug candidates. Here, we synthesised two enantiopure chiral ligands H2L1 and H2L2 (tetradentate cyclohexane-1,2-diamine-bridged bis(pyrrole-imine) derivatives). Metallation of the ligands with Au(III) afforded the chiral cationic complexes AuL1 and AuL2. The in vitro cytotoxicities of AuL1 and AuL2 determined in the NCI-60 single-dose drug screen were 56.5% and 89.1%, respectively. AuL1 was subsequently selected for a five-dose NCI-60 screen, attaining GI50, IC50, and LC50 values of 4.7, 9.3 and 39.8 μM, respectively. Hierarchical cluster analysis of the NCI-60 data indicated that the profile for AuL1 was similar to that of vinblastine sulfate, a microtubule-targeting vinca alkaloid. Reactions of AuL1 with glutathione (GSH) in vitro confirmed its susceptibility to reduction, Au(III) → Au(I), by intracellular thiols. Because human serum albumin (HSA) is responsible for transporting clinically deployed and investigational drugs, we studied the uptake of AuL1 and AuL2 by HSA to delineate how chirality impacts their protein-binding affinity. Steady-state fluorescence quenching data acquired on the native protein and data from site-specific probes showed that the compounds bind at sites close enough to Trp-214 (subdomain IIA) of HSA to quench the fluorophore. The bimolecular quenching rate constants, Kq, were ca. 102 times higher than the maximum diffusion-controlled collision constant of a biomolecule in water (1010 M-1 s-1), confirming that static fluorescence quenching was the dominant mechanism. The Stern-Volmer constants, KSV, were ∼104 M-1 at 37 °C, while the affinity constants, Ka (37 °C), measured ∼2.1 × 104 M-1 (AuL1) and ∼1.2 × 104 M-1 (AuL2) for enthalpy-driven ligand uptake targeting Sudlow's site I. Although far- and near-UV CD spectroscopy indicated that both complexes minimally perturb the secondary and tertiary structure of HSA, substantial shifts in the CD spectra were recorded for both protein-bound ligands. This study highlights the role of chirality in determining the cytotoxicity profiles and protein binding behaviour of enantiomeric Au(III) chelates.
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Affiliation(s)
- Sheldon Sookai
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO WITS 2050, Johannesburg, South Africa.
| | - Matthew P Akerman
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa
| | - Orde Q Munro
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO WITS 2050, Johannesburg, South Africa.
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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13
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Sofeo N, Toi MG, Ee EQG, Ng JY, Busran CT, Lukito BR, Thong A, Hermansen C, Peterson EC, Glitsos R, Arumugam P. Sustainable production of lipids from cocoa fatty acid distillate fermentation driven by adaptive evolution in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2024; 394:130302. [PMID: 38199440 DOI: 10.1016/j.biortech.2024.130302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Single cell oil production using oleaginous yeasts is a promising alternative to animal and plant-derived lipids. But substrate costs for microbial fermentation are a major bottleneck. Using side streams as alternative to substrates like glucose, for growing yeast, is a potential cost-effective solution. By combining a previously reported process of growing yeasts on a solid cocoa fatty acid distillate side stream with adaptive evolution techniques, the growth of oleaginous yeast Yarrowia lipolytica was improved by 2-fold. The lipid titre was also boosted by more than 3-fold. Using transcriptomics, key genes were identified that are possibly involved in tailoring of lipid composition, side stream utilisation and enhancement of lipid titres. Candidate genes were also identified that might enable efficient growth and utilization of fatty acids and triacylglycerides found in cocoa fatty acid distillate. In summary, this research has improved the understanding of side stream utilisation for lipid production in oleaginous yeast.
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Affiliation(s)
- Naazneen Sofeo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore.
| | - Min Gin Toi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - En Qi Grace Ee
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Jing Yang Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Coleen Toledo Busran
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Benedict Ryan Lukito
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Aaron Thong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Christian Hermansen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Eric Charles Peterson
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore; Institut National de la Recherche Scientifique - Eau Terre Environnement (INRS-ETE), 490 Rue de la Couronne, Quebec City, QC G1K 9A9, Canada
| | - Renata Glitsos
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Prakash Arumugam
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
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14
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Navina BK, Velmurugan NK, Senthil Kumar P, Rangasamy G, Palanivelu J, Thamarai P, Vickram AS, Saravanan A, Shakoor A. Fungal bioremediation approaches for the removal of toxic pollutants: Mechanistic understanding for biorefinery applications. CHEMOSPHERE 2024; 350:141123. [PMID: 38185426 DOI: 10.1016/j.chemosphere.2024.141123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/30/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Pollution is a global menace that poses harmful effects on all the living ecosystems and to the Earth. As years pass by, the available and the looming rate of pollutants increases at a faster rate. Although many treatments and processing strategies are waged for treating such pollutants, the by-products and the wastes or drain off generated by these treatments further engages in the emission of hazardous waste. Innovative and long-lasting solutions are required to address the urgent global issue of hazardous pollutant remediation from contaminated environments. Myco-remediation is a top-down green and eco-friendly tool for pollution management. It is a cost-effective and safer practice of converting pernicious substances into non-toxic forms by the use of fungi. But these pollutants can be transformed into useable products along with multiple benefits for the environment such as sequestration of carbon emissions and also to generate high valuable bioactive materials that fits as a sustainable economic model. The current study has examined the possible applications of fungi in biorefineries and their critical role in the transformation and detoxification of pollutants. The paper offers important insights into using fungal bioremediation for both economically and environmentally sound solutions in the domain of biorefinery applications by combining recent research findings.
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Affiliation(s)
- Bala Krishnan Navina
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, India
| | - Nandha Kumar Velmurugan
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, India
| | - P Senthil Kumar
- Centre for Pollution Control and Environmental Engineering, School of Engineering and Technology, Pondicherry University, Kalapet, Puducherry, 605014, India.
| | - Gayathri Rangasamy
- School of Engineering, Lebanese American University, Byblos, Lebanon; University Centre for Research and Development & Department of Civil Engineering, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Jeyanthi Palanivelu
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, India
| | - P Thamarai
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - A Saravanan
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - Awais Shakoor
- Hawkesbury Institute for the Environment, West Sydney University, Penrith, NSW, 2751, Australia
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15
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Rywińska A, Tomaszewska-Hetman L, Lazar Z, Juszczyk P, Sałata P, Malek K, Kawecki A, Rymowicz W. Application of New Yarrowia lipolytica Transformants in Production of Citrates and Erythritol from Glycerol. Int J Mol Sci 2024; 25:1475. [PMID: 38338753 PMCID: PMC10855631 DOI: 10.3390/ijms25031475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Citric acid and erythritol are obtained on an industrial scale using biotechnological methods. Due to the growing market demand for these products, research is underway to improve the process economics by introducing new microorganisms, in particular of the species Yarrowia lipolytica. The aim of this study was to evaluate transformants of Y. lipolytica for growth and ability to overproduce citric acids and erythritol from glycerol. The transformants were constructed by overexpressing glycerol kinase, methylcitrate synthase and mitochondrial succinate-fumarate transporter in the mutant Wratislavia 1.31. Next, strains were assessed for biosynthesis of citrate (pH 5.5; nitrogen limitation) and erythritol (pH 3.0; high osmotic pressure) from glycerol. Regardless of culture conditions strains, 1.31.GUT1/6 and 1.31.GUT1/6.CIT1/3 exhibited high rates of substrate utilization. Under conditions favoring citrate biosynthesis, both strains produced several percent more citrates, accompanied by higher erythritol production compared to the parental strain. During erythritol biosynthesis, the strain 1.31.GUT1/6.CIT1/3.E34672g obtained as a result of co-expression of all three genes stood out, producing 84.0 g/L of erythritol with yield and productivity of 0.54 g/g and 0.72 g/Lh, respectively, which places it in the group of the highest-ranked producers of erythritol among Y. lipolytica species.
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Affiliation(s)
| | - Ludwika Tomaszewska-Hetman
- Department of Biotechnology and Food Microbiology, The Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, Chełmońskiego Str. 37, 51-630 Wrocław, Poland; (A.R.); (Z.L.); (P.J.); (P.S.); (A.K.); (W.R.)
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16
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Miranda SM, Lopes M, Belo I. Exploring the use of hexadecane by Yarrowia lipolytica: Effect of dissolved oxygen and medium supplementation. J Biotechnol 2024; 380:29-37. [PMID: 38128617 DOI: 10.1016/j.jbiotec.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
This work aimed to evaluate the effect of medium composition and volumetric oxygen transfer coefficient (kLa) on Y. lipolytica growth and production of microbial lipids and enzymes from hexadecane. In the stirred tank bioreactor, increasing kLa from 11 h-1 to 132 h-1 improved the hexadecane assimilation rate, biomass concentration, and lipids synthesis (0.90 g·L-1). A cost-effective hexadecane-based medium supplemented with corn steep liquor and a low amount of ammonium sulfate boosted lipids production up to 2.1 g·L-1, composed of palmitic, palmitoleic, oleic, and linoleic acids. The unsaturated/saturated fraction was dependent on the C/N ratio. Lipids of Y. lipolytica CBS 2075 are promising feedstock for animal feed, food additives, or the biodiesel industry. Simultaneous synthesis of extracellular lipase and protease from hexadecane was observed, which is a new feature that was not previously reported. The highest enzyme activity was obtained at the highest C/N ratio conditions. These results open new perspectives on the application of Y. lipolytica-based cultures for the biotransformation of hexadecane-polluted streams into valuable compounds, fulfilling an interesting strategy towards the circular economy concept.
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Affiliation(s)
- Sílvia M Miranda
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Marlene Lopes
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Isabel Belo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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17
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Walker C, Mortensen M, Poudel B, Cotter C, Myers R, Okekeogbu IO, Ryu S, Khomami B, Giannone RJ, Laursen S, Trinh CT. Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals. mSystems 2023; 8:e0074123. [PMID: 37882587 PMCID: PMC10734471 DOI: 10.1128/msystems.00741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of Yarrowia lipolytica to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how Y. lipolytica activates its metabolism to utilize DP oil and establishes Y. lipolytica as a promising host for the upcycling of plastic wastes.
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Affiliation(s)
- Caleb Walker
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Max Mortensen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bindica Poudel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Christopher Cotter
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ryan Myers
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ikenna O. Okekeogbu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Seunghyun Ryu
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bamin Khomami
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Richard J. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Siris Laursen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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18
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Jagtap SS, Liu JJ, Walukiewicz HE, Riley R, Ahrendt S, Koriabine M, Cobaugh K, Salamov A, Yoshinaga Y, Ng V, Daum C, Grigoriev IV, Slininger PJ, Dien BS, Jin YS, Rao CV. Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiol Resour Announc 2023; 12:e0043523. [PMID: 37982613 PMCID: PMC10720525 DOI: 10.1128/mra.00435-23] [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: 05/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.
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Affiliation(s)
- Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Jing-Jing Liu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Hanna E. Walukiewicz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Steven Ahrendt
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Maxim Koriabine
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Kelly Cobaugh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Asaf Salamov
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Yuko Yoshinaga
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Igor V. Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Patricia J. Slininger
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Bruce S. Dien
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- Department of Food Science and Nutrition, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
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19
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Agrawal A, Yang Z, Blenner M. Engineering Yarrowia lipolytica for the biosynthesis of geraniol. Metab Eng Commun 2023; 17:e00228. [PMID: 38029016 PMCID: PMC10652127 DOI: 10.1016/j.mec.2023.e00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Geraniol is a monoterpene with wide applications in the food, cosmetics, and pharmaceutical industries. Microbial production has largely used model organisms lacking favorable properties for monoterpene production. In this work, we produced geraniol in metabolically engineered Yarrowia lipolytica. First, two plant-derived geraniol synthases (GES) from Catharanthus roseus (Cr) and Valeriana officinalis (Vo) were tested based on previous reports of activity. Both wild type and truncated mutants of GES (without signal peptide targeting chloroplast) were examined by co-expressing with MVA pathway enzymes tHMG1 and IDI1. Truncated CrGES (tCrGES) produced the most geraniol and thus was used for further experimentation. The initial strain was obtained by overexpression of the truncated HMG1, IDI and tCrGES. The acetyl-CoA precursor pool was enhanced by overexpressing mevalonate pathway genes such as ERG10, HMGS or MVK, PMK. The final strain overexpressing 3 copies of tCrGES and single copies of ERG10, HMGS, tHMG1, IDI produced approximately 1 g/L in shake-flask fermentation. This is the first demonstration of geraniol production in Yarrowia lipolytica and the highest de novo titer reported to date in yeast.
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Affiliation(s)
- Ayushi Agrawal
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
| | - Zhiliang Yang
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
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20
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Peterson EC, Siao R, Chua GG, Busran CT, Pavlovic R, Thong A, Hermansen C, Sofeo N, Kanagasundaram Y, Weingarten M, Lindley N. Single cell protein and oil production from solid cocoa fatty acid distillates co-fed ethanol. BIORESOURCE TECHNOLOGY 2023; 387:129630. [PMID: 37544531 DOI: 10.1016/j.biortech.2023.129630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
The use of solid lipid sidestreams have been overlooked as a feedstock for the production of microbial biomass for food and feed applications and little to no recent work has examined the utilization of solid fatty acid distillates (FADs), which are a significant residue from vegetable oil processing. Yarrowia lipolytica and Rhodosporidium toruloides cultivated on cocoa fatty acid distillates (CFAD) generated final cell dry weight values > 40 g/L, with strong productivity (3.3 g/L·h) and rich protein (>45%) and lipid content (>25%). Interestingly, microbial oils were > 65% unsaturated fatty acids, compared < 20% unsaturated content in FAD. Importantly, to overcome mass-transfer limitations associated with bioconversion of solid lipid residues, ethanol was applied as a co-substrate to solubilize FAD residues. Here, FAD residues from cocoa deodorization have been demonstrated to be high energy feedstocks that represent an attractive substrate for the production of both single cell protein and oil (SCPO).
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Affiliation(s)
- Eric Charles Peterson
- Institut National de la Recherche Scientifique - Eau Terre Environnement (INRS-ETE), 490 Rue de la Couronne, Quebec City, QC G1K 9A9, Canada; Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore.
| | - Rowanne Siao
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Gi Gi Chua
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Coleen Toledo Busran
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Renata Pavlovic
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Aaron Thong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Christian Hermansen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Naazneen Sofeo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Melanie Weingarten
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
| | - Nic Lindley
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Level 6, Nanos, Singapore 138669, Republic of Singapore
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21
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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22
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Messina E, de Souza CP, Cappella C, Barile SN, Scarcia P, Pisano I, Palmieri L, Nicaud JM, Agrimi G. Genetic inactivation of the Carnitine/Acetyl-Carnitine mitochondrial carrier of Yarrowia lipolytica leads to enhanced odd-chain fatty acid production. Microb Cell Fact 2023; 22:128. [PMID: 37443049 DOI: 10.1186/s12934-023-02137-8] [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: 03/31/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Mitochondrial carriers (MCs) can deeply affect the intracellular flux distribution of metabolic pathways. The manipulation of their expression level, to redirect the flux toward the production of a molecule of interest, is an attractive target for the metabolic engineering of eukaryotic microorganisms. The non-conventional yeast Yarrowia lipolytica is able to use a wide range of substrates. As oleaginous yeast, it directs most of the acetyl-CoA therefrom generated towards the synthesis of lipids, which occurs in the cytoplasm. Among them, the odd-chain fatty acids (OCFAs) are promising microbial-based compounds with several applications in the medical, cosmetic, chemical and agricultural industries. RESULTS In this study, we have identified the MC involved in the Carnitine/Acetyl-Carnitine shuttle in Y. lipolytica, YlCrc1. The Y. lipolytica Ylcrc1 knock-out strain failed to grow on ethanol, acetate and oleic acid, demonstrating the fundamental role of this MC in the transport of acetyl-CoA from peroxisomes and cytoplasm into mitochondria. A metabolic engineering strategy involving the deletion of YlCRC1, and the recombinant expression of propionyl-CoA transferase from Ralstonia eutropha (RePCT), improved propionate utilization and its conversion into OCFAs. These genetic modifications and a lipogenic medium supplemented with glucose and propionate as the sole carbon sources, led to enhanced accumulation of OCFAs in Y. lipolytica. CONCLUSIONS The Carnitine/Acetyl-Carnitine shuttle of Y. lipolytica involving YlCrc1, is the sole pathway for transporting peroxisomal or cytosolic acetyl-CoA to mitochondria. Manipulation of this carrier can be a promising target for metabolic engineering approaches involving cytosolic acetyl-CoA, as demonstrated by the effect of YlCRC1 deletion on OCFAs synthesis.
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Affiliation(s)
- Eugenia Messina
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, 78350, AgroParisTech, France
| | - Camilla Pires de Souza
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, 78350, AgroParisTech, France
| | - Claudia Cappella
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Simona Nicole Barile
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Isabella Pisano
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
- Bioenergetics and Molecular Biotechnologies (IBIOM), CNR Institute of Biomembranes, Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, 78350, AgroParisTech, France.
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy.
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23
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Urbanikova V, Park YK, Krajciova D, Tachekort M, Certik M, Grigoras I, Holic R, Nicaud JM, Gajdos P. Yarrowia lipolytica as a Platform for Punicic Acid Production. Int J Mol Sci 2023; 24:ijms24108823. [PMID: 37240172 DOI: 10.3390/ijms24108823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Punicic acid (PuA) is a polyunsaturated fatty acid with significant medical, biological, and nutraceutical properties. The primary source of punicic acid is the pomegranate seed oil obtained from fruits of trees that are mainly cultivated in subtropical and tropical climates. To establish sustainable production of PuA, various recombinant microorganisms and plants have been explored as platforms with limited efficiencies. In this study, the oleaginous yeast Yarrowia lipolytica was employed as a host for PuA production. First, growth and lipid accumulation of Y. lipolytica were evaluated in medium supplemented with pomegranate seed oil, resulting in the accumulation of lipids up to 31.2%, consisting of 22% PuA esterified in the fraction of glycerolipids. In addition, lipid-engineered Y. lipolytica strains, transformed with the bifunctional fatty acid conjugase/desaturase from Punica granatum (PgFADX), showed the ability to accumulate PuA de novo. PuA was detected in both polar and neutral lipid fractions, especially in phosphatidylcholine and triacylglycerols. Promoter optimization for PgFADX expression resulted in improved accumulation of PuA from 0.9 to 1.8 mg/g of dry cell weight. The best-producing strain expressing PgFADX under the control of a strong erythritol-inducible promoter produced 36.6 mg/L PuA. These results demonstrate that the yeast Y. lipolytica is a promising host for PuA production.
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Grants
- APVV-20-0166 INRAE, the French National Research Institute for Agriculture, Food and Environment, Micalis Institute, the Slovak Research and Development Agency
- VEGA 2/0012/20 Ministry of Education, Science, Research, and Sport of the Slovak Republic, and the Slovak Academy of Sciences
- NA Genopole, University of Evry-val-d'Essonne, University of Paris-Saclay, Investissements d'Avenir
- NA New England BioLabs (NEB)
- NA Integrated DNA Technologies Inc. (IDT)
- NA Twist Biosciences
- NA SnapGene
- NA Macherey Nagel
- NA Zymo Research
- NA Promega
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Affiliation(s)
- Veronika Urbanikova
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237 Bratislava, Slovakia
| | - Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Daniela Krajciova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Mehdi Tachekort
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Université Paris-Saclay, Univ Evry, CNRS, CEA, Génomique métabolique, 91057 Evry-Courcouronnes, France
| | - Milan Certik
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237 Bratislava, Slovakia
| | - Ioana Grigoras
- Université Paris-Saclay, Univ Evry, CNRS, CEA, Génomique métabolique, 91057 Evry-Courcouronnes, France
| | - Roman Holic
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Peter Gajdos
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237 Bratislava, Slovakia
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24
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Theodosiou E. Engineering Strategies for Efficient Bioconversion of Glycerol to Value-Added Products by Yarrowia lipolytica. Catalysts 2023. [DOI: 10.3390/catal13040657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Yarrowia lipolytica has been a valuable biotechnological workhorse for the production of commercially important biochemicals for over 70 years. The knowledge gained so far on the native biosynthetic pathways, as well as the availability of numerous systems and synthetic biology tools, enabled not only the regulation and the redesign of the existing metabolic pathways, but also the introduction of novel synthetic ones; further consolidating the position of the yeast in industrial biotechnology. However, for the development of competitive and sustainable biotechnological production processes, bioengineering should be reinforced by bioprocess optimization strategies. Although there are many published reviews on the bioconversion of various carbon sources to value-added products by Yarrowia lipolytica, fewer works have focused on reviewing up-to-date strain, medium, and process engineering strategies with an aim to emphasize the significance of integrated engineering approaches. The ultimate goal of this work is to summarize the necessary knowledge and inspire novel routes to manipulate at a systems level the yeast biosynthetic machineries by combining strain and bioprocess engineering. Due to the increasing surplus of biodiesel-derived waste glycerol and the favored glycerol-utilization metabolic pathways of Y. lipolytica over other carbon sources, the present review focuses on pure and crude glycerol-based biomanufacturing.
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25
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Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica. Biotechnol Adv 2023; 65:108128. [PMID: 36921878 DOI: 10.1016/j.biotechadv.2023.108128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
More than 200 million tons of plant oils and animal fats are produced annually worldwide from oil, crops, and the rendered animal fat industry. Triacylglycerol, an abundant energy-dense compound, is the major form of lipid in oils and fats. While oils or fats are very important raw materials and functional ingredients for food or related products, a significant portion is currently diverted to or recovered as waste. To significantly increase the value of waste oils or fats and expand their applications with a minimal environmental footprint, microbial biomanufacturing is presented as an effective strategy for adding value. Though both bacteria and yeast can be engineered to use oils or fats as the biomanufacturing feedstocks, the yeast Yarrowia lipolytica is presented as one of the most attractive platforms. Y. lipolytica is oleaginous, generally regarded as safe, demonstrated as a promising industrial producer, and has unique capabilities for efficient catabolism and bioconversion of lipid substrates. This review summarizes the major challenges and opportunities for Y. lipolytica as a new biomanufacturing platform for the production of value-added products from oils and fats. This review also discusses relevant cellular and metabolic engineering strategies such as fatty acid transport, fatty acid catabolism and bioconversion, redox balances and energy yield, cell morphology and stress response, and bioreaction engineering. Finally, this review highlights specific product classes including long-chain diacids, wax esters, terpenes, and carotenoids with unique synthesis opportunities from oils and fats in Y. lipolytica.
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26
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Homologous High-Level Lipase and Single-Cell Protein Production with Engineered Yarrowia lipolytica via Scale-Up Fermentation for Industrial Applications. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Yarrowia lipolytica is a promising feed additives. Here, we aimed to produce extracellular lipases and single-cell proteins (SCPs) at high levels simultaneously through fed-batch fermentation of engineered Y. lipolytica. The parameters for 500 mL shake flask cultures were optimized with a single factorial design. The resultant activity of lipase reached 880.6 U/mL after 84 h of fermentation, and 32.0 g/L fermentation broth of dry SCP was obtained at 120 h. To attain high SCP and lipase productivity, the high-density fed-batch fermentation of Y. lipolytica was scaled up in 10 L, 30 L, and 100 L fermentors. Using glycerol as the sole carbon source, the lipase activity peaked to 8083.3 U/mL, and the final dry SCP weight was 183.1 g/L at 94.6 h in 10 L fermentors. The extracellular lipase activity and SCP weight reached 11,100.0 U/mL and 173.3 g of dry SCP/L at 136 h in 30 L fermentors, respectively. Following 136 h of fed-batch fermentation, the extracellular lipase activity and dry SCP weight reached 8532.0 U/mL and 170.3 g/L in 100 L fermentors, respectively. A balance between the lipase secretion and growth of Y. lipolytica recombinant strain was achieved, indicating that an efficient fermentation strategy could promote further scale-up for industrial SCP production from engineered Y. lipolytica.
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27
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Utilization of n-alkane and roles of lipid transfer proteins in Yarrowia lipolytica. World J Microbiol Biotechnol 2023; 39:97. [PMID: 36781616 PMCID: PMC9925530 DOI: 10.1007/s11274-023-03541-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/15/2023]
Abstract
Yarrowia lipolytica, a dimorphic yeast belonging to the Ascomycota, has potent abilities to utilize hydrophobic compounds, such as n-alkanes and fatty acids, as carbon and energy sources. Yarrowia lipolytica can synthesize and accumulate large amounts of lipids, making it a promising host to produce various lipids and convert n-alkanes to useful compounds. For advanced use of Y. lipolytica in these applications, it is necessary to understand the metabolism of these hydrophobic compounds in this yeast and the underlying molecular mechanisms. In this review, current knowledge on the n-alkane metabolism and how this is regulated in Y. lipolytica is summarized. Furthermore, recent studies revealed that lipid transfer proteins are involved in the utilization of n-alkanes and the regulation of cell morphology in response to n-alkanes. This review discusses the roles of membrane lipids in these processes in Y. lipolytica.
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28
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Park YK, Ledesma-Amaro R. What makes Yarrowia lipolytica well suited for industry? Trends Biotechnol 2023; 41:242-254. [PMID: 35940976 DOI: 10.1016/j.tibtech.2022.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 01/24/2023]
Abstract
Yarrowia lipolytica possesses natural and engineered traits that make it a good host for the industrial bioproduction of chemicals, fuels, foods, and pharmaceuticals. In recent years, academic and industrial researchers have assessed its potential, developed synthetic biology techniques, improved its features, scaled its processes, and identified its limitations. Both publications and patents related to Y. lipolytica have shown a drastic increase during the past decade. Here, we discuss the characteristics of this yeast that make it suitable for industry and the remaining challenges for its wider use at large scale. We present evidence herein that shows the importance and potential of Y. lipolytica in bioproduction such that it may soon be one of the preferred choices of industry.
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Affiliation(s)
- Young-Kyoung Park
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK.
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29
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Selection of Yarrowia lipolytica Strains as Possible Solution to Valorize Untreated Cheese Whey. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cheese whey management and disposal is a major issue for dairy industries due to its high level of chemical and biochemical oxygen demand. However, it can still represent a source of nutrients (i.e., sugars, proteins and lipids) that can be applied, among other options, as substrate for microbial growth. Yarrowia lipolytica can grow in different environments, consuming both hydrophilic and hydrophobic substrates, and tolerates high salt concentrations. In this work, the lipolytic and proteolytic profile of 20 strains of Y. lipolytica were tested on caseins and butter. Then, their growth potential was evaluated in four types of whey (caciotta, ricotta, squacquerone and their mix). Y. lipolytica showed a very strain-dependent behavior for both hydrolytic profiles and growth capabilities on the different substrates. The best growers for all the types of whey tested were PO1, PO2, and RO2, with the first one reaching up to 8.77 log cfu/mL in caciotta whey after 72 h. The volatile molecule profile of the samples incubated with the best growers were characterized by higher amounts of esters, acids, ketones and alcohols. In this way, cheese whey can become a source of microbial cultures exploitable in the dairy sector.
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30
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Bigey F, Pasteur E, Połomska X, Thomas S, Crutz-Le Coq AM, Devillers H, Neuvéglise C. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. J Fungi (Basel) 2023; 9:jof9010076. [PMID: 36675897 PMCID: PMC9865632 DOI: 10.3390/jof9010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.
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Affiliation(s)
- Frédéric Bigey
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
| | - Emilie Pasteur
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xymena Połomska
- Department of Biotechnology & Food Microbiology, Wroclaw University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland
| | - Stéphane Thomas
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- IJPB, INRAE, 78000 Versailles, France
| | - Hugo Devillers
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- Correspondence:
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31
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Employing Engineered Enolase Promoter for Efficient Expression of Thermomyces lanuginosus Lipase in Yarrowia lipolytica via a Self-Excisable Vector. Int J Mol Sci 2022; 24:ijms24010719. [PMID: 36614159 PMCID: PMC9821249 DOI: 10.3390/ijms24010719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/03/2023] Open
Abstract
Yarrowia lipolytica is progressively being employed as a workhouse for recombinant protein expression. Here, we expanded the molecular toolbox by engineering the enolase promoter (pENO) and developed a new self-excisable vector, and based on this, a combined strategy was employed to enhance the expression of Thermomyces lanuginosus lipase (TLL) in Y. lipolytica. The strength of 11 truncated enolase promoters of different length was first identified using eGFP as a reporter. Seven of the truncated promoters were selected to examine their ability for driving TLL expression. Then, a series of enolase promoters with higher activities were developed by upstream fusing of different copies of UAS1B, and the recombinant strain Po1f/hp16e100-tll harboring the optimal promoter hp16e100 obtained a TLL activity of 447 U/mL. Additionally, a new self-excisable vector was developed based on a Cre/loxP recombination system, which achieved efficient markerless integration in Y. lipolytica. Subsequently, strains harboring one to four copies of the tll gene were constructed using this tool, with the three-copy strain Po1f/3tll showing the highest activity of 579 U/mL. The activity of Po1f/3tll was then increased to 720 U/mL by optimizing the shaking flask fermentation parameters. Moreover, the folding-related proteins Hac1, Pdi, and Kar2 were employed to further enhance TLL expression, and the TLL activity of the optimal recombinant strain Po1f/3tll-hac1-pdi-kar2 reached 1197 U/mL. By using this combined strategy, TLL activity was enhanced by approximately 39.9-fold compared to the initial strain. Thus, the new vector and the combined strategy could be a useful tool to engineer Y. lipolytica for high-level expression of heterologous protein.
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Biosurfactant Production from the Biodegradation of n-Paraffins, Isoprenoids and Aromatic Hydrocarbons from Crude Petroleum by Yarrowia lipolytica IMUFRJ 50682. FERMENTATION 2022. [DOI: 10.3390/fermentation9010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Yarrowia lipolytica is a unique, strictly aerobic yeast with the ability to degrade efficiently hydrophobic substrates. In the present work, we evaluated the degrading potential of Yarrowia lipolytica IMUFRJ 50682, isolated from tropical estuarine water in Rio de Janeiro (Brazil), and the possible biomolecules produced during this process. To investigate which crude oil compounds are degraded by Y. lipolytica IMUFRJ 50682, this microorganism was grown in a medium containing Marlim petroleum (19 °API, American Petroleum Institute gravity) at 28 °C and 160 rpm for 5 days. The residual petroleum was submitted to gas chromatograph-mass spectrometric analysis (GC-MS). The chromatographic fingerprints of the residual petroleum were compared with the abiotic control test incubated in the same conditions. Y. lipolytica assimilates high molecular weight hydrocarbons, such as n-alkanes (C11-C19), isoprenoids (pristane and phytane), aromatics with two or three aromatics rings (naphthalene, methylnaphthalenes, dimethylnaphthalenes, trimethylnaphthalenes, phenanthrene, methylphenanthrenes, dimethylphenanthrenes, anthracene). This strain was also capable of consuming more complex hydrocarbons, such as tricyclic terpanes. During this biodegradation, the emulsification index of the culture medium increased significantly, showing that biosurfactant molecules can be produced from this process. Therefore, Y. lipolytica IMUFRJ 50682 showed to be a potential crude oil degrading yeast, which can be used for bioremediation processes and simultaneously produce bioproducts of commercial interest.
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Nogueira JP, Souza IHDS, Andrade JKS, Narain N. Status of research on lactones used as aroma: A bibliometric review. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sales JCS, de Castro AM, Ribeiro BD, Coelho MAZ. Post-Consumer Poly(ethylene terephthalate) (PET) Depolymerization by Yarrowia lipolytica: A Comparison between Hydrolysis Using Cell-Free Enzymatic Extracts and Microbial Submerged Cultivation. Molecules 2022; 27:7502. [PMID: 36364329 PMCID: PMC9655755 DOI: 10.3390/molecules27217502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2024] Open
Abstract
Several microorganisms have been reported as capable of acting on poly(ethylene terephthalate) (PET) to some extent, such as Yarrowia lipolytica, which is a yeast known to produce various hydrolases of industrial interest. The present work aims to evaluate PET depolymerization by Y. lipolytica using two different strategies. In the first one, biocatalysts were produced during solid-state fermentation (SSF-YL), extracted and subsequently used for the hydrolysis of PET and bis(2-hydroxyethyl terephthalate) (BHET), a key intermediate in PET hydrolysis. Biocatalysts were able to act on BHET, yielding terephthalic acid (TPA) (131.31 µmol L-1), and on PET, leading to a TPA concentration of 42.80 µmol L-1 after 168 h. In the second strategy, PET depolymerization was evaluated during submerged cultivations of Y. lipolytica using four different culture media, and the use of YT medium ((w/v) yeast extract 1%, tryptone 2%) yielded the highest TPA concentration after 96 h (65.40 µmol L-1). A final TPA concentration of 94.3 µmol L-1 was obtained on a scale-up in benchtop bioreactors using YT medium. The conversion obtained in bioreactors was 121% higher than in systems with SSF-YL. The results of the present work suggest a relevant role of Y. lipolytica cells in the depolymerization process.
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Affiliation(s)
- Julio Cesar Soares Sales
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149. Ilha do Fundão, Rio de Janeiro 21941-909, Brazil
| | - Aline Machado de Castro
- Divisão de Biotecnologia, Centro de Pesquisa e Desenvolvimento, PETROBRAS, Av. Horácio Macedo, 950. Ilha do Fundão, Rio de Janeiro 21941-915, Brazil
| | - Bernardo Dias Ribeiro
- Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149. Ilha do Fundão, Rio de Janeiro 21941-909, Brazil
| | - Maria Alice Zarur Coelho
- Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149. Ilha do Fundão, Rio de Janeiro 21941-909, Brazil
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Diamantopoulou P, Papanikolaou S. Biotechnological production of sugar-alcohols: focus on Yarrowia lipolytica and edible/medicinal mushrooms. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Angelicola MV, Fernández PM, Aybar MJ, Van Nieuwenhove CP, Figueroa LI, Viñarta SC. Bioconversion of commercial and crude glycerol to single-cell oils by the Antarctic yeast Rhodotorula glutinis R4 as a biodiesel feedstock. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Onésime D, Vidal L, Thomas S, Henry C, Martin V, André G, Kubiak P, Minard P, Celinska E, Nicaud JM. A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica. Microb Cell Fact 2022; 21:200. [PMID: 36182920 PMCID: PMC9526294 DOI: 10.1186/s12934-022-01925-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yarrowia lipolytica, a nonconventional oleaginous yeast species, has attracted attention due to its high lipid degradation and accumulation capacities. Y. lipolytica is used as a chassis for the production of usual and unusual lipids and lipid derivatives. While the genes involved in the intracellular transport and activation of fatty acids in different cellular compartments have been characterized, no genes involved in fatty acid transport from the extracellular medium into the cell have been identified thus far. In this study, we identified secreted proteins involved in extracellular fatty acid binding. RESULTS Recent analysis of the Y. lipolytica secretome led to the identification of a multigene family that encodes four secreted proteins, preliminarily named UP1 to UP4. These proteins were efficiently overexpressed individually in wild-type and multideletant strain (Q4: Δup1Δup2Δup3Δup4) backgrounds. Phenotypic analysis demonstrated the involvement of these proteins in the binding of extracellular fatty acids. Additionally, gene deletion and overexpression prevented and promoted sensitivity to octanoic acid (C8) toxicity, respectively. The results suggested binding is dependent on aliphatic chain length and fatty acid concentration. 3D structure modeling supports the proteins' role in fatty acid assimilation at the molecular level. CONCLUSIONS We discovered a family of extracellular-fatty-acid-binding proteins in Y. lipolytica and have proposed to name its members eFbp1 to eFbp4. The exact mode of eFbps action remains to be deciphered individually and synergistically; nevertheless, it is expected that the proteins will have applications in lipid biotechnology, such as improving fatty acid production and/or bioconversion.
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Affiliation(s)
- Djamila Onésime
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Léa Vidal
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Stéphane Thomas
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Véronique Martin
- INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gwenaëlle André
- INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Piotr Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Philippe Minard
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Ewelina Celinska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Jean-Marc Nicaud
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,INRAE-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France.
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Onyeaka H, Anumudu CK, Okpe C, Okafor A, Ihenetu F, Miri T, Odeyemi OA, Anyogu A. Single Cell Protein for Foods and Feeds: A Review of Trends. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2206160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Introduction:
Predictions on the world’s population in the next few decades suggest that the global demand for animal-derived proteins may not be met if current conventional agriculture approaches are used. One promising solution to this complex crisis lies in the use of single-cell proteins (SCP). SCP refers to the edible biomass of unicellular microorganisms and can be developed as animal feeds or human foods. This paper provides a detailed overview on research towards the production and utilisation of SCPs and trends within the field.
Study Design:
A bibliometric based study was conducted on 425 SCP research articles collected from the Web of Science database, analysing the most cited papers using VOSviewer software, and contributing authors, affiliations and country of origin. Research publications on SCP started in 1961 and has grown steadily over the years.
Discussion:
Emerging research topics within SCP production focused on the use of improved fungal strains, the composition and characteristics of SCPs based on the type of substrates used, industrial production processes and the use of waste for SCP production, which serves the dual purpose of mitigating the cost associated with waste disposal and production of a valuable product.
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Vyas S, Matsakas L, Rova U, Christakopoulos P, Patel A. Insights into hydrophobic waste valorization for the production of value-added oleochemicals. Microb Biotechnol 2022; 16:177-183. [PMID: 35932161 PMCID: PMC9871509 DOI: 10.1111/1751-7915.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 01/27/2023] Open
Affiliation(s)
- Sachin Vyas
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Leonidas Matsakas
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Ulrika Rova
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Paul Christakopoulos
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Alok Patel
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
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Lipid Readjustment in Yarrowia lipolytica Odd-Chain Fatty Acids Producing Strains. Biomolecules 2022; 12:biom12081026. [PMID: 35892336 PMCID: PMC9394261 DOI: 10.3390/biom12081026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Yarrowia lipolytica is a promising oleaginous yeast for producing unusual lipids, such as odd-chain fatty acids (OCFA). Their diverse applications and low natural production make OCFA particularly interesting. In recent studies, inhibiting the catabolic pathway of precursor, boosting precursor pools, and optimizing substrate combination greatly improved the production of OCFA in Y. lipolytica. We explored the lipid readjustment of OCFA in engineered Y. lipolytica strains. NPLC-Corona-CAD® evidenced a time-dependent overproduction of free fatty acids, diglycerides, and phosphatidylcholine (PC) in obese LP compared to obese L. Phosphatidylethanolamine (PE) and phosphatidylinositol, largely overproduced in obese LP at 72 h compared to obese L, vanished at 216 h. The fatty acyls (FAs) composition of glycero- and glycerophospholipids was determined by NPLC-APPI+-HRMS from in-source generated monoacylglycerol-like fragment ions. C18:1 and C17:1 were predominant acylglycerols in obese L and obese LP, respectively. Phosphatidic acid, PE, and PC exhibited similar FAs composition but differed in their molecular species distributions. Cardiolipin (CL) is known to contain mostly C18:2 FAs corresponding to the composition in obese L, 50% of C18:2, and 35% of C18:1. In obese LP, both FAs dropped to drop to 20%, and C17:1 were predominant, reaching 55%. We hypothesize that CL-modified composition in obese LPs may alter mitochondrial function and limit lipid production.
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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Bhutada G, Menard G, Bhunia RK, Hapeta PP, Ledesma-Amaro R, Eastmond PJ. Production of human milk fat substitute by engineered strains of Yarrowia lipolytica. Metab Eng Commun 2022; 14:e00192. [PMID: 35036316 PMCID: PMC8752951 DOI: 10.1016/j.mec.2022.e00192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/09/2021] [Accepted: 01/03/2022] [Indexed: 01/05/2023] Open
Abstract
Human milk fat has a distinctive stereoisomeric structure where palmitic acid is esterified to the middle (sn-2) position on the glycerol backbone of the triacylglycerol and unsaturated fatty acids to the outer (sn-1/3) positions. This configuration allows for more efficient nutrient absorption in the infant gut. However, the fat used in most infant formulas originates from plants, which exclude palmitic acid from the sn-2 position. Oleaginous yeasts provide an alternative source of lipids for human nutrition. However, these yeasts also exclude palmitic acid from the sn-2 position of their triacylglycerol. Here we show that Yarrowia lipolytica can be engineered to produce triacylglycerol with more than 60% of the palmitic acid in the sn-2 position, by expression of lysophosphatidic acid acyltransferases with palmitoyl-Coenzyme A specificity. The engineered Y. lipolytica strains can be cultured on glycerol, glucose, palm oil or a mixture of substrates, under nitrogen limited condition, to produce triacylglycerol with a fatty acid composition that resembles human milk fat, in terms of the major molecular species (palmitic, oleic and linoleic acids). Culture on palm oil or a mixture of glucose and palm oil produced the highest lipid titre and a triacylglycerol composition that is most similar with human milk fat. Our data show that an oleaginous yeast can be engineered to produce a human milk fat substitute (β-palmitate), that could be used as an ingredient in infant formulas.
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Affiliation(s)
- Govindprasad Bhutada
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Guillaume Menard
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Rupam Kumar Bhunia
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India
| | - Piotr P. Hapeta
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Peter J. Eastmond
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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Syed N, Singh S, Chaturvedi S, Nannaware AD, Khare SK, Rout PK. Production of lactones for flavoring and pharmacological purposes from unsaturated lipids: an industrial perspective. Crit Rev Food Sci Nutr 2022; 63:10047-10078. [PMID: 35531939 DOI: 10.1080/10408398.2022.2068124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The enantiomeric pure and natural (+)-Lactones (C ≤ 14) with aromas obtained from fruits and milk are considered flavoring compounds. The flavoring value is related to the lactones' ring size and chain length, which blend in varying concentrations to produce different stone-fruit flavors. The nature-identical and enantiomeric pure (+)-lactones are only produced through whole-cell biotransformation of yeast. The industrially important γ-decalactone and δ-decalactone are produced by a four-step aerobic-oxidation of ricinoleic acid (RA) following the lactonization mechanism. Recently, metabolic engineering strategies have opened up new possibilities for increasing productivity. Another strategy for increasing yield is to immobilize the RA and remove lactones from the broth regularly. Besides flavor impact, γ-, δ-, ε-, ω-lactones of the carbon chain (C8-C12), the macro-lactones and their derivatives are vital in pharmaceuticals and healthcare. These analogues are isolated from natural sources or commercially produced via biotransformation and chemical synthesis processes for medicinal use or as active pharmaceutical ingredients. The various approaches to biotransformation have been discussed in this review to generate more prospects from a commercial point of view. Finally, this work will be regarded as a magical brick capable of containing both traditional and genetic engineering technology while contributing to a wide range of commercial applications.
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Affiliation(s)
- Naziya Syed
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Suman Singh
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Shivani Chaturvedi
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | - Ashween Deepak Nannaware
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, Uttar Pradesh, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | - Prasant Kumar Rout
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, Uttar Pradesh, India
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Kolhe N, Damle E, Pradhan A, Zinjarde S. A comprehensive assessment of Yarrowia lipolytica and its interactions with metals: Current updates and future prospective. Biotechnol Adv 2022; 59:107967. [PMID: 35489656 DOI: 10.1016/j.biotechadv.2022.107967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022]
Abstract
The non-conventional yeast Yarrowia lipolytica has been popular as a model system for understanding biological processes such as dimorphism and lipid accumulation. The organism can efficiently utilize hydrophobic substrates (hydrocarbons and triglycerides) thereby rendering it relevant in bioremediation of oil polluted environments. The current review focuses on the interactions of this fungus with metal pollutants and its potential application in bioremediation of metal contaminated locales. This fungus is intrinsically equipped with a variety of physiological and biochemical features that enable it to tide over stress conditions induced by the presence of metals. Production of enzymes such as phosphatases, reductases and superoxide dismutases are worth a special mention. In the presence of metals, levels of inherently produced metal binding proteins (metallothioneins) and the pigment melanin are seen to be elevated. Morphological alterations with respect to biofilm formation and dimorphic transition from yeast to mycelial form are also induced by certain metals. The biomass of Y. lipolytica is inherently important as a biosorbent and cell surface modification, process optimization or whole cell immobilization techniques have aided in improving this capability. In the presence of metals such as mercury, cadmium, copper and uranium, the culture forms nanoparticulate deposits. In addition, on account of its intrinsic reductive ability, Y. lipolytica is being exploited for synthesizing nanoparticles of gold, silver, cadmium and selenium with applications as antimicrobial compounds, location agents for bioimaging and as feed supplements. This versatile organism thus has great potential in interacting with various metals and addressing problems related to their pollutant status.
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Affiliation(s)
- Nilesh Kolhe
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune 411007, India
| | - Eeshan Damle
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune 411007, India
| | - Aditya Pradhan
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune 411007, India
| | - Smita Zinjarde
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune 411007, India.
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Pereira AS, Lopes M, Miranda SM, Belo I. Bio-oil production for biodiesel industry by Yarrowia lipolytica from volatile fatty acids in two-stage batch culture. Appl Microbiol Biotechnol 2022; 106:2869-2881. [PMID: 35394162 DOI: 10.1007/s00253-022-11900-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 11/26/2022]
Abstract
Microbial lipids-derived biodiesel is garnering much attention owing to its potential to substitute diesel fuel. In this study, lipid accumulation by Yarrowia lipolytica from volatile fatty acids (VFAs) was studied in a lab-scale stirred tank bioreactor. In batch cultures, Y. lipolytica NCYC 2904 was able to grow in 18 g·L-1 of VFAs (acetate, propionate, and butyrate), and the addition of a co-substrate (glucose) led to a fivefold improvement in lipid concentration. Furthermore, the two-stage batch culture (growth phase in glucose (1st stage) followed by a lipogenic phase in VFAs (2nd stage)) was the best strategy to obtain the highest lipid content in the cells (37%, w/w), with aeration conditions that kept dissolved oxygen concentration between 40% and 50% of saturation during the lipogenic phase. The estimated fuel properties of biodiesel produced from Y. lipolytica NCYC 2904 lipids are comparable with those of the biodiesel produced from vegetable oils and are in accordance with the international standards (EN 14214 and ASTM D6751). The cultivation strategies herein devised enable a sustainable, eco-friendly, and economical production of microbial lipids, based on feedstocks such as VFAs that can be derived from the acidogenic fermentation of organic wastes. KEY POINTS: • Addition of glucose to VFAs enhances lipids in Y. lipolytica in batch cultures • Two-stage batch culture - growth in glucose followed by VFAs pulse - rises lipids • Dissolved oxygen of 40-50% of saturation is crucial at the lipogenic phase.
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Affiliation(s)
- Ana S Pereira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Marlene Lopes
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Sílvia M Miranda
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Belo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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Bouhia Y, Hafidi M, Ouhdouch Y, El Boukhari MEM, El Fels L, Zeroual Y, Lyamlouli K. Microbial Community Succession and Organic Pollutants Removal During Olive Mill Waste Sludge and Green Waste Co-composting. Front Microbiol 2022; 12:814553. [PMID: 35265049 PMCID: PMC8899611 DOI: 10.3389/fmicb.2021.814553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Olive mill wastewater sludge (OMWS) is the main by-product of the olive industry. OMWS is usually dumped in landfills without prior treatment and may cause several eco-environmental hazards due to its high toxicity, which is mainly attributed to polyphenols and lipids. OMWS is rich in valuable biocompounds, which makes it highly desirable for valorization by composting. However, there is a need to understand how microbial communities evolve during OMWS composting with respect to physicochemical changes and the dynamics of pollutant degradation. In this study, we addressed the relationship between microbial community, physicochemical variations and pollutants degradation during the co-composting of OMWS and green wastes using metagenomic- and culture-dependent approaches. The results showed that in raw OMWS, Pichia was the most represented genus with almost 53% of the total identified fungal population. Moreover, the bacteria that dominated were Zymobacter palmae (20%) and Pseudomonas sp. (19%). The addition of green waste to OMWS improved the actinobacterial diversity of the mixture and enhanced the degradation of lipids (81.3%) and polyphenols (84.54%). Correlation analysis revealed that Actinobacteria and fungi (Candida sp., Galactomyces sp., and Pichia manshurica) were the microorganisms that had the greatest influence on the composting process. Overall, these findings provide for the first time some novel insights into the microbial dynamics during OMWS composting and may contribute to the development of tailored inoculum for process optimization.
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Affiliation(s)
- Youness Bouhia
- Laboratory of Microbial Biotechnology, Agrosciences and Environment, Labelled Research Unit-CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco.,Biodiversity and Plant Sciences Program, AgroBioSciences Department, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
| | - Mohamed Hafidi
- Laboratory of Microbial Biotechnology, Agrosciences and Environment, Labelled Research Unit-CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco.,Biodiversity and Plant Sciences Program, AgroBioSciences Department, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
| | - Yedir Ouhdouch
- Laboratory of Microbial Biotechnology, Agrosciences and Environment, Labelled Research Unit-CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco.,Biodiversity and Plant Sciences Program, AgroBioSciences Department, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
| | - Mohammed El Mehdi El Boukhari
- Laboratory of Microbial Biotechnology, Agrosciences and Environment, Labelled Research Unit-CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco.,Biodiversity and Plant Sciences Program, AgroBioSciences Department, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
| | - Loubna El Fels
- Laboratory of Microbial Biotechnology, Agrosciences and Environment, Labelled Research Unit-CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | | | - Karim Lyamlouli
- Biodiversity and Plant Sciences Program, AgroBioSciences Department, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
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Abstract
Today, food valorization represents an important challenge to environmental sustainability. Food waste can be used as a substrate for single cell protein production suitable for animal feed. In this study, animal and agricultural food waste, represented by fish, pineapple, banana, apple, and citrus peels, have been used simultaneously as a fermentation substrate for single cell protein production by Saccharomyces cerevisiae, to evaluate the possibility of using a multi complex substrate for a simultaneous biovalorization of different food waste. The fermentation process was implemented by the supplementation of a hydrolytic enzyme and nutrient to allow the best yeast growing conditions. At the end of the process, the final substrate was enriched in protein, reaching up to 40.19% of protein, making the multisubstrate useful for animal feed. The substrate was also investigated for crude lipid, ash, lignin, soluble and insoluble sugar. The substrate composition at the end of the fermentation process was represented by 14.46% of crude lipid, 1.08% ash, 6.29% lignin. Conversely, the soluble and insoluble sugars dropped down from 20.5% to 6.10% and 19.15% to 2.14%, respectively, at the end of the process.
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A Temporal Evolution Perspective of Lipase Production by Yarrowia lipolytica in Solid-State Fermentation. Processes (Basel) 2022. [DOI: 10.3390/pr10020381] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lipases are enzymes that, in aqueous or non-aqueous media, act on water-insoluble substrates, mainly catalyzing reactions on carboxyl ester bonds, such as hydrolysis, aminolysis, and (trans)esterification. Yarrowia lipolytica is a non-conventional yeast known for secreting lipases and other bioproducts; therefore, it is of great interest in various industrial fields. The production of lipases can be carried on solid-state fermentation (SSF) that utilizes solid substrates in the absence, or near absence, of free water and presents minimal problems with microbial contamination due to the low water contents in the medium. Moreover, SSF offers high volumetric productivity, targets concentrated compounds, high substrate concentration tolerance, and has less wastewater generation. In this sense, the present work provides a temporal evolution perspective regarding the main aspects of lipase production in SSF by Y. lipolytica, focusing on the most relevant aspects and presenting the potential of such an approach.
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Raman-probes for monitoring metabolites and nutrient fate in Yarrowia lipolytica using deuterated glucose. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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