1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Qin J, Kurt E, LBassi T, Sa L, Xie D. Biotechnological production of omega-3 fatty acids: current status and future perspectives. Front Microbiol 2023; 14:1280296. [PMID: 38029217 PMCID: PMC10662050 DOI: 10.3389/fmicb.2023.1280296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Omega-3 fatty acids, including alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have shown major health benefits, but the human body's inability to synthesize them has led to the necessity of dietary intake of the products. The omega-3 fatty acid market has grown significantly, with a global market from an estimated USD 2.10 billion in 2020 to a predicted nearly USD 3.61 billion in 2028. However, obtaining a sufficient supply of high-quality and stable omega-3 fatty acids can be challenging. Currently, fish oil serves as the primary source of omega-3 fatty acids in the market, but it has several drawbacks, including high cost, inconsistent product quality, and major uncertainties in its sustainability and ecological impact. Other significant sources of omega-3 fatty acids include plants and microalgae fermentation, but they face similar challenges in reducing manufacturing costs and improving product quality and sustainability. With the advances in synthetic biology, biotechnological production of omega-3 fatty acids via engineered microbial cell factories still offers the best solution to provide a more stable, sustainable, and affordable source of omega-3 fatty acids by overcoming the major issues associated with conventional sources. This review summarizes the current status, key challenges, and future perspectives for the biotechnological production of major omega-3 fatty acids.
Collapse
Affiliation(s)
| | | | | | | | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, United States
| |
Collapse
|
6
|
Zvonarev AN, Trilisenko LV, Farofonova VV, Kulakovskaya EV, Abashina TN, Dmitriev VV, Kulakovskaya T. The Extracellular Vesicles Containing Inorganic Polyphosphate of Candida Yeast upon Growth on Hexadecane. J Xenobiot 2023; 13:529-543. [PMID: 37873811 PMCID: PMC10594515 DOI: 10.3390/jox13040034] [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: 07/31/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
The cell wall of Candida yeast grown on presence of hexadecane as a sole carbon source undergoes structural and functional changes including the formation of specific supramolecular complexes-canals. The canals contain specific polysaccharides and enzymes that provide primary oxidization of alkanes. In addition, inorganic polyphosphate (polyP) was identified in Candida maltosa canals. The aim of the work was a comparative study of the features of cell walls and extracellular structures in yeast C. maltosa, C. albicans and C. tropicalis with special attention to inorganic polyphosphates as possible part of these structures when grown on the widely used xenobiotic hexadecane (diesel fuel). Fluorescence microscopy with DAPI has shown an unusual localization of polyP on the cell surface and in the exovesicles in the three yeast species, when growing on hexadecane. Electron-scanning microscopy showed that the exovesicles were associated with the cell wall and also presented in the external environment probably as biofilm components. Treatment of hexadecane-grown cells with purified Ppx1 polyphosphatase led to the release of phosphate into the incubation medium and the disappearance of polyP in vesicles and cell wall observed using microscopic methods. The results indicate the important role of polyP in the formation of extracellular structures in the Candida yeast when consuming hexadecane and are important for the design of xenobiotic destructors based on yeast or mixed cultures.
Collapse
Affiliation(s)
- Anton N. Zvonarev
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (A.N.Z.); (L.V.T.); (E.V.K.); (V.V.D.); (T.K.)
| | - Ludmila V. Trilisenko
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (A.N.Z.); (L.V.T.); (E.V.K.); (V.V.D.); (T.K.)
| | - Vasilina V. Farofonova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Ekaterina V. Kulakovskaya
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (A.N.Z.); (L.V.T.); (E.V.K.); (V.V.D.); (T.K.)
| | - Tatiana N. Abashina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (A.N.Z.); (L.V.T.); (E.V.K.); (V.V.D.); (T.K.)
| | - Vladimir V. Dmitriev
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (A.N.Z.); (L.V.T.); (E.V.K.); (V.V.D.); (T.K.)
| | - Tatiana Kulakovskaya
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (A.N.Z.); (L.V.T.); (E.V.K.); (V.V.D.); (T.K.)
| |
Collapse
|
7
|
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.
Collapse
|
8
|
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.
Collapse
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:
| |
Collapse
|
9
|
OUP accepted manuscript. FEMS Yeast Res 2022; 22:6522173. [DOI: 10.1093/femsyr/foac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 01/20/2022] [Accepted: 02/02/2022] [Indexed: 11/12/2022] Open
|
10
|
Tenagy, Iwama R, Kobayashi S, Shiwa Y, Yoshikawa H, Horiuchi H, Fukuda R, Kajiwara S. Acyl-CoA synthetases, Aal4 and Aal7, are involved in the utilization of exogenous fatty acids in Yarrowia lipolytica. J GEN APPL MICROBIOL 2021; 67:9-14. [PMID: 33100277 DOI: 10.2323/jgam.2020.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The yeast Yarrowia lipolytica assimilates hydrophobic compounds, such as n-alkanes and fatty acids, as sole carbon and energy sources. It has been shown that the acyl-CoA synthetase (ACS) genes, FAT1 and FAA1, are involved in the activation of fatty acids produced during the metabolism of n-alkanes, but the ACS genes that are involved in the metabolism of fatty acids from the culture medium remains to be identified. In this paper, we have identified the ACS genes involved in the utilization of exogenous fatty acids. RNA-seq analysis and qRT-PCR revealed that the transcript levels of the peroxisomal ACS-like protein-encoding genes AAL4 and AAL7 were increased in the presence of oleic acid. The single deletion mutant of AAL4 or AAL7 and double deletion mutant of AAL4 and AAL7 did not show any defects in the growth on the medium containing glucose, glycerol, n-alkanes, or fatty acids. In contrast, the mutant with deletion of seven genes, FAA1, FAT1-FAT4, AAL4, and AAL7, showed severe growth defects on the medium containing dodecanoic acid or oleic acid. These results suggest that Aal4p and Aal7p play important roles in the metabolism of exogenous fatty acids in collaboration with Faa1p and Fat1p-Fat4p.
Collapse
Affiliation(s)
- Tenagy
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Ryo Iwama
- Department of Biotechnology, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | | | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture.,Department of Molecular Microbiology, Tokyo University of Agriculture
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture.,Department of Bioscience, Tokyo University of Agriculture
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Susumu Kajiwara
- School of Life Science and Technology, Tokyo Institute of Technology
| |
Collapse
|
11
|
Mamaev D, Zvyagilskaya R. Yarrowia lipolytica: a multitalented yeast species of ecological significance. FEMS Yeast Res 2021; 21:6141120. [PMID: 33595651 DOI: 10.1093/femsyr/foab008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/13/2021] [Indexed: 02/07/2023] Open
Abstract
Yarrowia lipolytica is characterized by GRAS (Generally regarded as safe) status, the versatile substrate utilization profile, rapid utilization rates, metabolic diversity and flexibility, the unique abilities to tolerate to extreme environments (acidic, alkaline, hypersaline, heavy metal-pollutions and others) and elevated biosynthesis and secreting capacities. These advantages of Y. lipolytica allow us to consider it as having great ecological significance. Unfortunately, there is still a paucity of relevant review data. This mini-review highlights ecological ubiquity of Y. lipolytica species, their ability to diversify and colonize specialized niches. Different Y. lipolytica strains, native and engineered, are beneficial in degrading many environmental pollutants causing serious ecological problems worldwide. In agriculture has a potential to be a bio-control agent by stimulating plant defense response, and an eco-friendly bio-fertilizer. Engineered strains of Y. lipolytica have become a very promising platform for eco-friendly production of biofuel, commodities, chemicals and secondary metabolites of plant origin, obtaining which by other method were limited or economically infeasible, or were accompanied by stringent environmental problems. Perspectives to use potential of Y. lipolytica's capacities for industrial scale production of valuable compounds in an eco-friendly manner are proposed.
Collapse
Affiliation(s)
- Dmitry Mamaev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
| | - Renata Zvyagilskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
| |
Collapse
|
12
|
Changes in cell wall structure and protein set in Candida maltosa grown on hexadecane. Folia Microbiol (Praha) 2020; 66:247-253. [PMID: 33247329 DOI: 10.1007/s12223-020-00840-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022]
Abstract
The yeast Candida maltosa is a model organism for studying adaptive changes in the structure and function of the cell wall when consuming water-insoluble nutrient sources. The cells of C. maltosa that utilize hydrocarbons contain supramolecular structures, so-called "canals" in the cell wall. Differences in protein profiles of culture liquids and cell wall extracts of C. maltosa grown on glucose and hexadecane were analyzed. Three proteins specific of cells grown on hexadecane were revealed using mass spectrometry: glycosyl hydrolase EPD2 in the culture liquid; a protein belonging to the cytochrome C family in the 0.5 mol/L NaCl extract; and PPIA_CANAL protein known as chaperone, in the 0.1% SDS extract. The possible role of these proteins in cell wall structures responsible for adaptation to hexadecane utilization is discussed.
Collapse
|
13
|
Wang J, Ledesma-Amaro R, Wei Y, Ji B, Ji XJ. Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica - A Review. BIORESOURCE TECHNOLOGY 2020; 313:123707. [PMID: 32595069 DOI: 10.1016/j.biortech.2020.123707] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Current energy security and climate change policies encourage the development and utilization of bioenergy. Oleaginous yeasts provide a particularly attractive platform for the sustainable production of biofuels and industrial chemicals due to their ability to accumulate high amounts of lipids. In particular, microbial lipids in the form of triacylglycerides (TAGs) produced from renewable feedstocks have attracted considerable attention because they can be directly used in the production of biodiesel and oleochemicals analogous to petrochemicals. As an oleaginous yeast that is generally regarded as safe, Yarrowia lipolytica has been extensively studied, with large amounts of data on its lipid metabolism, genetic tools, and genome sequencing and annotation. In this review, we highlight the newest strategies for increasing lipid accumulation using metabolic engineering and summarize the research advances on the overaccumulation of lipids in Y. lipolytica. Finally, perspectives for future engineering approaches are proposed.
Collapse
Affiliation(s)
- Jinpeng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of State Ministry of Education, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, People's Republic of China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
| |
Collapse
|
14
|
Wanderley LAS, Bergamo VZ, Machado GRM, Mendes RMO, Valente P, Fuentefria AM. Influence of detergents and sodium hypochlorite on Yarrowia lipolytica biofilms in utensils used in industrial production of colonial cheese. AN ACAD BRAS CIENC 2020; 92:e20181379. [PMID: 32756842 DOI: 10.1590/0001-3765202020181379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/07/2019] [Indexed: 11/22/2022] Open
Abstract
The formation of microbial biofilms in materials used in the industrial production of dairy may lead to deterioration of these foods. Yarrowia lipolytica biofilms are widely found in dairy products and can modify the final characteristics of these products. Thus, this study investigated the effectiveness of hygienization by detergents and sodium hypochlorite on the formation of Y. lipolytica biofilms in different utensils usually employed during industrial cheese production, like polypropylene, hoses, and nylon/polyethylene. The utensils were sanitized using solutions of mild and alkaline detergents, and sodium hypochlorite, according to the cheese industry Standard Operation Procedure. Results showed that in all coupons there was biofilm formation with Y. lipolytica isolates. The contact angle measurements were favored to promote the adhesion of the biofilm in the evaluated surfaces. Even after treatment with sanitizers, a significant survival rate of planktonic cells was observed in all coupons tested. These results indicate that Y. lipolytica biofilms show a significant ability to adhere to polypropylene, presenting an important impact on the quality of colonial cheese.
Collapse
Affiliation(s)
- Liliane A S Wanderley
- Universidade Federal do Rio Grande do Sul/UFRGS, Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Rua Sarmento Leite, 500, Bairro Farroupilha, 90050-170 Porto Alegre, RS, Brazil.,Universidade Comunitária da Região de Chapecó - UNOCHAPECÓ, Laboratório de Microbiologia, Avenida Senador Atílio Fontana, 591-E Efapi, Bairro Engenho Braun, 89809-000 Chapecó, SC, Brazil
| | - Vanessa Z Bergamo
- Universidade Federal do Rio Grande do Sul/UFRGS, Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Rua Sarmento Leite, 500, Bairro Farroupilha, 90050-170 Porto Alegre, RS, Brazil
| | - Gabriella R M Machado
- Universidade Federal do Rio Grande do Sul/UFRGS, Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Rua Sarmento Leite, 500, Bairro Farroupilha, 90050-170 Porto Alegre, RS, Brazil
| | - Rose Maria O Mendes
- Universidade Comunitária da Região de Chapecó - UNOCHAPECÓ, Laboratório de Microbiologia, Avenida Senador Atílio Fontana, 591-E Efapi, Bairro Engenho Braun, 89809-000 Chapecó, SC, Brazil
| | - PatrÍcia Valente
- Universidade Federal do Rio Grande do Sul/UFRGS, Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Rua Sarmento Leite, 500, Bairro Farroupilha, 90050-170 Porto Alegre, RS, Brazil
| | - Alexandre M Fuentefria
- Universidade Federal do Rio Grande do Sul/UFRGS, Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Rua Sarmento Leite, 500, Bairro Farroupilha, 90050-170 Porto Alegre, RS, Brazil
| |
Collapse
|
15
|
Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts. Sci Rep 2020; 10:10269. [PMID: 32581293 PMCID: PMC7314818 DOI: 10.1038/s41598-020-67200-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/07/2020] [Indexed: 01/16/2023] Open
Abstract
Cytochrome P450s from the CYP52 family participate in the assimilation of alkanes and fatty acids in fungi. In this work, the evolutionary history of a set of orthologous and paralogous CYP52 proteins from Saccharomycetales yeasts was inferred. Further, the phenotypic assimilation profiles were related with the distribution of cytochrome CYP52 members among species. The maximum likelihood phylogeny of CYP52 inferred proteins reveled a frequent ancient and modern duplication and loss events that generated orthologous and paralogous groups. Phylogeny and assimilation profiles of alkanes and fatty acids showed a family expansion in yeast isolated from hydrophobic-rich environments. Docking analysis of deduced ancient CYP52 proteins suggests that the most ancient function was the oxidation of C4-C11 alkanes, while the oxidation of >10 carbon alkanes and fatty acids is a derived character. The ancient CYP52 paralogs displayed partial specialization and promiscuous interaction with hydrophobic substrates. Additionally, functional optimization was not evident. Changes in the interaction of ancient CYP52 with different alkanes and fatty acids could be associated with modifications in spatial orientations of the amino acid residues that comprise the active site. The extended family of CYP52 proteins is likely evolving toward functional specialization, and certain redundancy for substrates is being maintained.
Collapse
|
16
|
Microbial production of (2 R ,3 S )-isocitric acid: state of the arts and prospects. Appl Microbiol Biotechnol 2019; 103:9321-9333. [DOI: 10.1007/s00253-019-10207-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/11/2019] [Accepted: 10/19/2019] [Indexed: 12/13/2022]
|
17
|
Yarrowia lipolytica: more than an oleaginous workhorse. Appl Microbiol Biotechnol 2019; 103:9251-9262. [DOI: 10.1007/s00253-019-10200-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
|
18
|
Suematsu R, Miyamoto T, Saijo S, Yamasaki S, Tada Y, Yoshida H, Miyake Y. Identification of lipophilic ligands of Siglec5 and -14 that modulate innate immune responses. J Biol Chem 2019; 294:16776-16788. [PMID: 31551352 DOI: 10.1074/jbc.ra119.009835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/02/2019] [Indexed: 01/22/2023] Open
Abstract
Sialic acid-binding immunoglobulin-like lectins (Siglecs) are a family of cell-surface immune receptors that bind to sialic acid at terminal glycan residues. Siglecs also recognize nonsialic acid ligands, many of which remain to be characterized. Here, we found that Siglec5 and Siglec14 recognize lipid compounds produced by Trichophyton, a fungal genus containing several pathogenic species. Biochemical approaches revealed that the Siglec ligands are fungal alkanes and triacylglycerols, an unexpected finding that prompted us to search for endogenous lipid ligands of Siglecs. Siglec5 weakly recognized several endogenous lipids, but the mitochondrial lipid cardiolipin and the anti-inflammatory lipid 5-palmitic acid-hydroxystearic acid exhibited potent ligand activity on Siglec5. Further, the hydrophobic stretch in the Siglec5 N terminus region was found to be required for efficient recognition of these lipids. Notably, this hydrophobic stretch was dispensable for recognition of sialic acid. Siglec5 inhibited cell activation upon ligand binding, and accordingly, the lipophilic ligands suppressed interleukin-8 (IL-8) production in Siglec5-expressing human monocytic cells. Siglec14 and Siglec5 have high sequence identity in the extracellular region, and Siglec14 also recognized the endogenous lipids. However, unlike Siglec5, Siglec14 transduces activating signals upon ligand recognition. Indeed, the endogenous lipids induced IL-8 production in Siglec14-expressing human monocytic cells. These results indicated that Siglec5 and Siglec14 can recognize lipophilic ligands that thereby modulate innate immune responses. To our knowledge, this is the first study reporting the binding of Siglecs to lipid ligands, expanding our understanding of the biological function and importance of Siglecs in the innate immunity.
Collapse
Affiliation(s)
- Rie Suematsu
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan.,Department of Rheumatology, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Tomofumi Miyamoto
- Department of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Shinobu Saijo
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Sho Yamasaki
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.,Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
| | - Yoshifumi Tada
- Department of Rheumatology, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Hiroki Yoshida
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Yasunobu Miyake
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| |
Collapse
|
19
|
Trotter PJ, Juco K, Le HT, Nelson K, Tamayo LI, Nicaud JM, Park YK. Glutamate dehydrogenases in the oleaginous yeast Yarrowia lipolytica. Yeast 2019; 37:103-115. [PMID: 31119792 DOI: 10.1002/yea.3425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/17/2019] [Indexed: 11/12/2022] Open
Abstract
Glutamate dehydrogenases (GDHs) are fundamental to cellular nitrogen and energy balance. Yet little is known about these enzymes in the oleaginous yeast Yarrowia lipolytica. The YALI0F17820g and YALI0E09603g genes, encoding potential GDH enzymes in this organism, were examined. Heterologous expression in gdh-null Saccharomyces cerevisiae and examination of Y. lipolytica strains carrying gene deletions demonstrate that YALI0F17820g (ylGDH1) encodes a NADP-dependent GDH whereas YALI0E09603g (ylGDH2) encodes a NAD-dependent GDH enzyme. The activity encoded by these two genes accounts for all measurable GDH activity in Y. lipolytica. Levels of the two enzyme activities are comparable during logarithmic growth on rich medium, but the NADP-ylGDH1p enzyme activity is most highly expressed in stationary and nitrogen starved cells by threefold to 12-fold. Replacement of ammonia with glutamate causes a decrease in NADP-ylGdh1p activity, whereas NAD-ylGdh2p activity is increased. When glutamate is both carbon and nitrogen sources, the activity of NAD-ylGDH2p becomes dominant up to 18-fold compared with that of NADP-ylGDH1p. Gene deletion followed by growth on different carbon and nitrogen sources shows that NADP-ylGdh1p is required for efficient nitrogen assimilation whereas NAD-ylGdh2p plays a role in nitrogen and carbon utilization from glutamate. Overexpression experiments demonstrate that ylGDH1 and ylGDH2 are not interchangeable. These studies provide a vital basis for future consideration of how these enzymes function to facilitate energy and nitrogen homeostasis in Y. lipolytica.
Collapse
Affiliation(s)
- Pamela J Trotter
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Karen Juco
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Ha T Le
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Kjersten Nelson
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Lizeth I Tamayo
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Jean-Marc Nicaud
- Biologie intégrative du Métabolisme Lipidique, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Young-Kyoung Park
- Biologie intégrative du Métabolisme Lipidique, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
20
|
Ortiz-Álvarez J, Vera-Ponce de León A, Trejo-Cerro O, Vu HT, Chávez-Camarillo G, Villa-Tanaca L, Hernández-Rodríguez C. Candida pseudoglaebosa and Kodamaea ohmeri are capable of degrading alkanes in the presence of heavy metals. J Basic Microbiol 2019; 59:792-806. [PMID: 31368594 DOI: 10.1002/jobm.201900027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/01/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023]
Abstract
The aim of this study was to examine four strains of two yeast species in relation to their capability for assimilating alkanes in the presence of heavy metals (HMs). The four strains tested were Candida pseudoglaebosa ENCB-7 and Kodamaea ohmeri ENCB-8R, ENCB-23, and ENCB-VIK. Determination was made of the expression of CYP52 genes involved in alkane hydroxylation. When exposed to Cu2+ , Zn2+ , Pb2+ , Cd2+ , and As3+ at pH 3 and 5, all four strains could assimilate several n-alkanes having at least six carbon atoms. The three K. ohmeri strains could also utilize branched alkanes, cycloalkanes, and n-octanol as sole carbon sources. Kinetic assays demonstrated greater biomass production and specific growth of the yeasts exposed to long-chain n-alkanes. Fragments of paralogous CYP52 genes of C. pseudoglaebosa ENCB-7 and K. ohmeri ENCB-23 were amplified, sequenced, and phylogenetically evaluated. Reverse-transcription polymerase chain reaction revealed that n-nonane and n-decane induced to CpCYP52-G3, CpCYP52-G9, and CpCYP52-G10. KoCYP52-G3 was induced with n-decane and n-octanol. Also, CpCYP52-G3 and CpCYP52-G9 were induced by glucose. In conclusion, C. pseudoglaebosa and K. ohmeri were able to degrade several alkanes in the presence of HMs and under acidic conditions. These yeasts harbor paralogous alkane-induced CYP52 genes, which display different profiles of transcriptional expression.
Collapse
Affiliation(s)
- Jossue Ortiz-Álvarez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo Vera-Ponce de León
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Oscar Trejo-Cerro
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Hoa T Vu
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Griselda Chávez-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| |
Collapse
|
21
|
Ortiz-Álvarez J, Vera-Ponce de León A, Trejo-Cerro O, Vu HT, Chávez-Camarillo G, Villa-Tanaca L, Hernández-Rodríguez C. Candida pseudoglaebosa and Kodamaea ohmeri are capable of degrading alkanes in the presence of heavy metals. J Basic Microbiol 2019. [PMID: 31183881 DOI: 10.1002/jobm.jobm201900027] [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: 01/15/2019] [Revised: 05/01/2019] [Accepted: 05/16/2019] [Indexed: 11/11/2022]
Abstract
The aim of this study was to examine four strains of two yeast species in relation to their capability for assimilating alkanes in the presence of heavy metals (HMs). The four strains tested were Candida pseudoglaebosa ENCB-7 and Kodamaea ohmeri ENCB-8R, ENCB-23, and ENCB-VIK. Determination was made of the expression of CYP52 genes involved in alkane hydroxylation. When exposed to Cu2+ , Zn2+ , Pb2+ , Cd2+ , and As3+ at pH 3 and 5, all four strains could assimilate several n-alkanes having at least six carbon atoms. The three K. ohmeri strains could also utilize branched alkanes, cycloalkanes, and n-octanol as sole carbon sources. Kinetic assays demonstrated greater biomass production and specific growth of the yeasts exposed to long-chain n-alkanes. Fragments of paralogous CYP52 genes of C. pseudoglaebosa ENCB-7 and K. ohmeri ENCB-23 were amplified, sequenced, and phylogenetically evaluated. Reverse-transcription polymerase chain reaction revealed that n-nonane and n-decane induced to CpCYP52-G3, CpCYP52-G9, and CpCYP52-G10. KoCYP52-G3 was induced with n-decane and n-octanol. Also, CpCYP52-G3 and CpCYP52-G9 were induced by glucose. In conclusion, C. pseudoglaebosa and K. ohmeri were able to degrade several alkanes in the presence of HMs and under acidic conditions. These yeasts harbor paralogous alkane-induced CYP52 genes, which display different profiles of transcriptional expression.
Collapse
Affiliation(s)
- Jossue Ortiz-Álvarez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo Vera-Ponce de León
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Oscar Trejo-Cerro
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Hoa T Vu
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Griselda Chávez-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| |
Collapse
|
22
|
Gálvez-López D, Chávez-Meléndez B, Vázquez-Ovando A, Rosas-Quijano R. The metabolism and genetic regulation of lipids in the oleaginous yeast Yarrowia lipolytica. Braz J Microbiol 2019; 50:23-31. [PMID: 30637631 PMCID: PMC6863248 DOI: 10.1007/s42770-018-0004-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/02/2018] [Indexed: 01/08/2023] Open
Abstract
The biotechnological potential of Yarrowia lipolytica, as a single cell oil-producing microorganism, is presented in this review. Although initially this yeast species was considered as a lipid-degrading, recently, it was reclassified as a lipid-producing microorganism, since it has been reported to be capable of accumulating diverse desirable fatty acids after metabolic pathway engineering. In the first part of the present document, a general revision of the oil metabolic pathways and the capacity of oil production in Y. lipolytica is presented. The single cell oil produced by these metabolic engineering strategies has been designed by optimization, introduction, or suppression of new pathways to increase yield on lipid production. Later on, the genetic regulation systems and the lipid composition generated by this yeast for industrial purposes are discussed. These lipids could be safely used in the chemical food and biofuel industries, due to their high proportion of oleic acid. This document emphasizes in the overviewing at Y. lipolytica as an ideal oil cell factory, and as an excellent model to produce single cell oil.
Collapse
Affiliation(s)
- Didiana Gálvez-López
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Tapachula, Chiapas, México
| | - Bianca Chávez-Meléndez
- Unidad Académica Multidisciplinaria, Universidad Autónoma de Tamaulipas, Reynosa, México
| | | | | |
Collapse
|
23
|
Osh6p, a homologue of the oxysterol-binding protein, is involved in production of functional cytochrome P450 belonging to CYP52 family in n-alkane-assimilating yeast Yarrowia lipolytica. Biochem Biophys Res Commun 2018; 499:836-842. [DOI: 10.1016/j.bbrc.2018.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/01/2018] [Indexed: 01/04/2023]
|
24
|
Huang Z, Lei K, He D, Xu Y, Williams J, Hu L, McNeil M, Ruso JM, Liu Z, Guo Z, Wang Z. Self-regulation in chemical and bio-engineering materials for intelligent systems. CAAI TRANSACTIONS ON INTELLIGENCE TECHNOLOGY 2018; 3:40-48. [PMID: 34113747 PMCID: PMC8188858 DOI: 10.1049/trit.2018.0004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Herein, the authors review the self-regulation system secured by well-designed hybrid materials, composites, and complex system. As a broad concept, the self-regulated material/system has been defined in a wide research field and proven to be of great interest for use in a biomedical system, mechanical system, physical system, as the fact of something such as an organisation regulating itself without intervention from external perturbation. Here, they focus on the most recent discoveries of self-regulation phenomenon and progress in utilising the self-regulation design. This paper concludes by examining various practical applications of the remarkable materials and systems including manipulation of the oil/water interface, cell out-layer structure, radical activity, electron energy level, and mechanical structure of nanomaterials. From material science to bioengineering, self-regulation proves to be not only viable, but increasingly useful in many applications. As part of intelligent engineering, self-regulatory materials are expected to be more used as integrated intelligent components.
Collapse
Affiliation(s)
- Zhongyuan Huang
- Chemistry Department, Xavier University of Louisiana, New Orleans, LA 70125, USA
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, Henan, People’s Republic of China
| | - Kewei Lei
- Chemistry Department, Xavier University of Louisiana, New Orleans, LA 70125, USA
- Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, People’s Republic of China
| | - Dan He
- Chemistry Department, Xavier University of Louisiana, New Orleans, LA 70125, USA
- Department of Pharmaceutical Analysis, Chongqing Medical University, Chongqing 400016, People’s Republic of China
| | - Yanbin Xu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, Shandong, People’s Republic of China
| | - Jacob Williams
- Department of Physics and Engineering, Frostburg State University, Frostburg, MD 21532, USA
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA
| | - Liu Hu
- Integrated Composites Laboratory (ICL), Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
- National Engineering Research Center for Advanced Polymer Processing Technology, Zhengzhou University, Zhengzhou 450002, People’s Republic of China
| | - Macy McNeil
- Chemistry Department, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Juan M. Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Zhen Liu
- Department of Physics and Engineering, Frostburg State University, Frostburg, MD 21532, USA
| | - Zhanhu Guo
- Integrated Composites Laboratory (ICL), Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Zhe Wang
- Chemistry Department, Xavier University of Louisiana, New Orleans, LA 70125, USA
| |
Collapse
|
25
|
Xie D. Integrating Cellular and Bioprocess Engineering in the Non-Conventional Yeast Yarrowia lipolytica for Biodiesel Production: A Review. Front Bioeng Biotechnol 2017; 5:65. [PMID: 29090211 PMCID: PMC5650997 DOI: 10.3389/fbioe.2017.00065] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/02/2017] [Indexed: 12/14/2022] Open
Abstract
As one of the major biofuels to replace fossil fuel, biodiesel has now attracted more and more attention due to its advantages in higher energy density and overall less greenhouse gas generation. Biodiesel (fatty acid alkyl esters) is produced by chemically or enzymatically catalyzed transesterification of lipids from microbial cells, microalgae, oil crops, or animal fats. Currently, plant oils or waste cooking oils/fats remain the major source for biodiesel production via enzymatic route, but the production capacity is limited either by the uncertain supplement of plant oils or by the low or inconsistent quality of waste oils/fats. In the past decades, significant progresses have been made on synthesis of microalgae oils directly from CO2via a photosynthesis process, but the production cost from any current technologies is still too high to be commercialized due to microalgae’s slow growth rate on CO2, inefficiency in photo-bioreactors, lack of efficient contamination control methods, and high cost in downstream recovery. At the same time, many oleaginous microorganisms have been studied to produce lipids via the fatty acid synthesis pathway under aerobic fermentation conditions, among them one of the most studied is the non-conventional yeast, Yarrowia lipolytica, which is able to produce fatty acids at very high titer, rate, and yield from various economical substrates. This review summarizes the recent research progresses in both cellular and bioprocess engineering in Y. lipolytica to produce lipids at a low cost that may lead to commercial-scale biodiesel production. Specific technologies include the strain engineering for using various substrates, metabolic engineering in high-yield lipid synthesis, cell morphology study for efficient substrate uptake and product formation, free fatty acid formation and secretion for improved downstream recovery, and fermentation engineering for higher productivities and less operating cost. To further improve the economics of the microbial oil-based biodiesel, production of lipid-related or -derived high-value products are also discussed.
Collapse
Affiliation(s)
- Dongming Xie
- Massachusetts Biomanufacturing Center, Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, United States
| |
Collapse
|
26
|
Lee H, Sugiharto YEC, Lee S, Park G, Han C, Jang H, Jeon W, Park H, Ahn J, Kang K, Lee H. Characterization of the newly isolated ω-oxidizing yeast Candida sorbophila DS02 and its potential applications in long-chain dicarboxylic acid production. Appl Microbiol Biotechnol 2017; 101:6333-6342. [PMID: 28589225 DOI: 10.1007/s00253-017-8321-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/18/2017] [Accepted: 04/29/2017] [Indexed: 12/13/2022]
Abstract
α, ω-Dicarboxylic acids (DCAs) are multipurpose chemicals widely used in polymers, perfumes, plasticizers, lubricants, and adhesives. The biotransformation of DCAs from alkanes and fatty acids by microorganisms has attracted recent interest, since synthesis via chemical oxidation causes problems in terms of the environment and safety. We isolated an ω-oxidizing yeast from a wastewater disposal facility of a petrochemical factory by chemostat enrichment culture. The haploid strain identified as Candida sorbophila DS02 grew on glucose and dodecane, exhibiting greater cell shrinkage on the latter. In flask cultures with mixed alkanes (C10-16) and fatty acid methyl esters (C10-16), DS02 used mixed alkanes simultaneously unlike Candida tropicalis and Yarrowia lipolytica and showed high substrate resistance. In flask cultures with acrylic acid-a known inhibitor of β-oxidation-DS02 produced 0.28 g/l dodecanedioic acid (DDDA) from dodecane, similar to wild-type C. tropicalis ATCC 20336. In fed-batch fermentation, DS02 produced 9.87 g/l DDDA, which was 5.7-fold higher than wild-type C. tropicalis. These results suggest that C. sorbophila strain DS02 has potential applications for the large-scale production of DCA.
Collapse
Affiliation(s)
- Heeseok Lee
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Yohanes Eko Chandra Sugiharto
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Seunghoon Lee
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Gyuyeon Park
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Changpyo Han
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Hyeran Jang
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Heejoon Park
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Jungoh Ahn
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Kyungbo Kang
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Hongwoen Lee
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea.
| |
Collapse
|
27
|
Δ12-fatty acid desaturase is involved in growth at low temperature in yeast Yarrowia lipolytica. Biochem Biophys Res Commun 2017; 488:165-170. [DOI: 10.1016/j.bbrc.2017.05.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/04/2017] [Indexed: 12/19/2022]
|
28
|
Zvonarev AN, Crowley DE, Ryazanova LP, Lichko LP, Rusakova TG, Kulakovskaya TV, Dmitriev VV. Cell wall canals formed upon growth of Candida maltosa in the presence of hexadecane are associated with polyphosphates. FEMS Yeast Res 2017; 17:3798215. [DOI: 10.1093/femsyr/fox026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 05/01/2017] [Indexed: 01/01/2023] Open
|
29
|
Ledesma-Amaro R, Nicaud JM. Metabolic Engineering for Expanding the Substrate Range of Yarrowia lipolytica. Trends Biotechnol 2016; 34:798-809. [DOI: 10.1016/j.tibtech.2016.04.010] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
|
30
|
Iwama R, Kobayashi S, Ishimaru C, Ohta A, Horiuchi H, Fukuda R. Functional roles and substrate specificities of twelve cytochromes P450 belonging to CYP52 family in n-alkane assimilating yeast Yarrowia lipolytica. Fungal Genet Biol 2016; 91:43-54. [PMID: 27039152 DOI: 10.1016/j.fgb.2016.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/26/2022]
Abstract
Yarrowia lipolytica possesses twelve ALK genes, which encode cytochromes P450 in the CYP52 family. In this study, using a Y. lipolytica strain from which all twelve ALK genes had been deleted, strains individually expressing each of the ALK genes were constructed and their roles and substrate specificities were determined by observing their growth on n-alkanes and analyzing fatty acid metabolism. The results suggested that the twelve Alk proteins can be categorized into four groups based on their substrate specificity: Alk1p, Alk2p, Alk9p, and Alk10p, which have significant activities to hydroxylate n-alkanes; Alk4p, Alk5p, and Alk7p, which have significant activities to hydroxylate the ω-terminal end of dodecanoic acid; Alk3p and Alk6p, which have significant activities to hydroxylate both n-alkanes and dodecanoic acid; and Alk8p, Alk11p, and Alk12p, which showed faint or no activities to oxidize these substrates. The involvement of Alk proteins in the oxidation of fatty alcohols and fatty aldehydes was also analyzed by measuring viability of the mutant deleted for twelve ALK genes in medium containing dodecanol and by observing growth on dodecanal of a mutant strain, in which twelve ALK genes were deleted along with four fatty aldehyde dehydrogenase genes. It was suggested that ALK gene(s) is/are involved in the detoxification of dodecanol and the assimilation of dodecanal. These results imply that genes encoding CYP52-family P450s have undergone multiplication and diversification in Y. lipolytica for assimilation of various hydrophobic compounds.
Collapse
Affiliation(s)
- Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kobayashi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chiaki Ishimaru
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, 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.
| |
Collapse
|
31
|
Liu HH, Ji XJ, Huang H. Biotechnological applications of Yarrowia lipolytica: Past, present and future. Biotechnol Adv 2015; 33:1522-46. [DOI: 10.1016/j.biotechadv.2015.07.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 07/13/2015] [Accepted: 07/29/2015] [Indexed: 01/01/2023]
|
32
|
Zhu Q, Jackson EN. Metabolic engineering of Yarrowia lipolytica for industrial applications. Curr Opin Biotechnol 2015; 36:65-72. [DOI: 10.1016/j.copbio.2015.08.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/18/2015] [Accepted: 08/09/2015] [Indexed: 01/01/2023]
|
33
|
Masuda M, Oshima A, Noguchi T, Kagiwada S. Induction of intranuclear membranes by overproduction of Opi1p and Scs2p, regulators for yeast phospholipid biosynthesis, suggests a mechanism for Opi1p nuclear translocation. J Biochem 2015; 159:351-61. [PMID: 26590299 DOI: 10.1093/jb/mvv105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the expression of phospholipid biosynthetic genes is suppressed by the Opi1p negative regulator. Opi1p enters into the nucleoplasm from the nuclear membrane to suppress the gene expression under repressing conditions. The binding of Opi1p to the nuclear membrane requires an integral membrane protein, Scs2p and phosphatidic acid (PA). Although it is demonstrated that the association of Opi1p with membranes is affected by PA levels, how Opi1p dissociates from Scs2p is unknown. Here, we found that fluorescently labelled Opi1p accumulated on a perinuclear region in an Scs2p-dependent manner. Electron microscopic analyses indicated that the perinuclear region consists of intranuclear membranes, which may be formed by the invagination of the nuclear membrane due to the accumulation of Opi1p and Scs2p in a restricted area. As expected, localization of Opi1p and Scs2p in the intranuclear membranes was detected by immunoelectron microscopy. Biochemical analysis showed that Opi1p recovered in the membrane fraction was detergent insoluble while Scs2p was soluble, implying that Opi1p behaves differently from Scs2p in the fraction. We hypothesize that Opi1p dissociates from Scs2p after targeting to the nuclear membrane, making it possible to be released from the membrane quickly when PA levels decrease.
Collapse
Affiliation(s)
- Miki Masuda
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| | - Ayaka Oshima
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| | - Tetsuko Noguchi
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| | - Satoshi Kagiwada
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| |
Collapse
|
34
|
Kobayashi S, Tezaki S, Horiuchi H, Fukuda R, Ohta A. Acidic phospholipid-independent interaction of Yas3p, an Opi1-family transcriptional repressor ofYarrowia lipolytica, with the endoplasmic reticulum. Yeast 2015; 32:691-701. [DOI: 10.1002/yea.3096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
| | - Satoshi Tezaki
- Department of Biotechnology; The University of Tokyo; Japan
| | | | | | - Akinori Ohta
- Department of Biotechnology; The University of Tokyo; Japan
| |
Collapse
|
35
|
Tenagy, Park JS, Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Involvement of acyl-CoA synthetase genes in n-alkane assimilation and fatty acid utilization in yeast Yarrowia lipolytica. FEMS Yeast Res 2015; 15:fov031. [PMID: 26019148 DOI: 10.1093/femsyr/fov031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we investigated the roles of YAL1 (FAA1) and FAT1 encoding acyl-CoA synthetases (ACSs) and three additional orthologs of ACS genes FAT2-FAT4 of the yeast Yarrowia lipolytica in the assimilation or utilization of n-alkanes and fatty acids. ACS deletion mutants were generated to characterize their function. The FAT1 deletion mutant exhibited decreased growth on n-alkanes of 10-18 carbons, whereas the FAA1 mutant showed growth reduction on n-alkane of 16 carbons. However, FAT2-FAT4 deletion mutants did not show any growth defects, suggesting that FAT1 and FAA1 are involved in the activation of fatty acids produced during the metabolism of n-alkanes. In contrast, deletions of FAA1 and FAT1-FAT4 conferred no defect in growth on fatty acids. The wild-type strain grew in the presence of cerulenin, an inhibitor of fatty acid synthesis, by utilizing exogenously added fatty acid or fatty acid derived from n-alkane when oleic acid or n-alkane of 18 carbons was supplemented. However, the FAA1 deletion mutant did not grow, indicating a critical role for FAA1 in the utilization of fatty acids. Fluorescent microscopic observation and biochemical analyses suggested that Fat1p is present in the peroxisome and Faa1p is localized in the cytosol and to membranes.
Collapse
Affiliation(s)
- Tenagy
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun Seok Park
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kobayashi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, 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
| |
Collapse
|
36
|
Yarrowia lipolytica: recent achievements in heterologous protein expression and pathway engineering. Appl Microbiol Biotechnol 2015; 99:4559-77. [PMID: 25947247 DOI: 10.1007/s00253-015-6624-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/13/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica has become a recognized system for expression/secretion of heterologous proteins. This non-conventional yeast is currently being developed as a workhorse for biotechnology by several research groups throughout the world, especially for single-cell oil production, whole cell bioconversion and upgrading of industrial wastes. This mini-review presents established tools for protein expression in Y. lipolytica and highlights novel developments in the areas of promoter design, surface display, and host strain or metabolic pathway engineering. An overview of the industrial and commercial biotechnological applications of Y. lipolytica is also presented.
Collapse
|
37
|
Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Alcohol dehydrogenases and an alcohol oxidase involved in the assimilation of exogenous fatty alcohols in Yarrowia lipolytica. FEMS Yeast Res 2015; 15:fov014. [DOI: 10.1093/femsyr/fov014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
|
38
|
Yuzbasheva EY, Yuzbashev TV, Mostova EB, Perkovskaya NI, Sineokii SP. Microbial synthesis of biodiesel and its prospects. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814090075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Fatty aldehyde dehydrogenase multigene family involved in the assimilation of n-alkanes in Yarrowia lipolytica. J Biol Chem 2014; 289:33275-86. [PMID: 25315778 DOI: 10.1074/jbc.m114.596890] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the n-alkane assimilating yeast Yarrowia lipolytica, n-alkanes are oxidized to fatty acids via fatty alcohols and fatty aldehydes, after which they are utilized as carbon sources. Here, we show that four genes (HFD1-HFD4) encoding fatty aldehyde dehydrogenases (FALDHs) are involved in the metabolism of n-alkanes in Y. lipolytica. A mutant, in which all of four HFD genes are deleted (Δhfd1-4 strain), could not grow on n-alkanes of 12-18 carbons; however, the expression of one of those HFD genes restored its growth on n-alkanes. Production of Hfd2Ap or Hfd2Bp, translation products of transcript variants generated from HFD2 by the absence or presence of splicing, also supported the growth of the Δhfd1-4 strain on n-alkanes. The FALDH activity in the extract of the wild-type strain was increased when cells were incubated in the presence of n-decane, whereas this elevation in FALDH activity by n-decane was not observed in Δhfd1-4 strain extract. Substantial FALDH activities were detected in the extracts of Escherichia coli cells expressing the HFD genes. Fluorescent microscopic observation suggests that Hfd3p and Hfd2Bp are localized predominantly in the peroxisome, whereas Hfd1p and Hfd2Ap are localized in both the endoplasmic reticulum and the peroxisome. These results suggest that the HFD multigene family is responsible for the oxidation of fatty aldehydes to fatty acids in the metabolism of n-alkanes, and raise the possibility that Hfd proteins have diversified by gene multiplication and RNA splicing to efficiently assimilate or detoxify fatty aldehydes in Y. lipolytica.
Collapse
Affiliation(s)
- Ryo Iwama
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Satoshi Kobayashi
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Akinori Ohta
- the Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Ryouichi Fukuda
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| |
Collapse
|
40
|
Dulermo R, Gamboa-Meléndez H, Dulermo T, Thevenieau F, Nicaud JM. The fatty acid transport protein Fat1p is involved in the export of fatty acids from lipid bodies inYarrowia lipolytica. FEMS Yeast Res 2014; 14:883-96. [DOI: 10.1111/1567-1364.12177] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022] Open
Affiliation(s)
- Rémi Dulermo
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | - Heber Gamboa-Meléndez
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | - Thierry Dulermo
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | | | - Jean-Marc Nicaud
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| |
Collapse
|
41
|
Zinjarde S, Apte M, Mohite P, Kumar AR. Yarrowia lipolytica and pollutants: Interactions and applications. Biotechnol Adv 2014; 32:920-33. [PMID: 24780156 DOI: 10.1016/j.biotechadv.2014.04.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/21/2014] [Accepted: 04/18/2014] [Indexed: 11/25/2022]
Abstract
Yarrowia lipolytica is a dimorphic, non-pathogenic, ascomycetous yeast species with distinctive physiological features and biochemical characteristics that are significant in environment-related matters. Strains naturally present in soils, sea water, sediments and waste waters have inherent abilities to degrade hydrocarbons such as alkanes (short and medium chain) and aromatic compounds (biphenyl and dibenzofuran). With the application of slow release fertilizers, design of immobilization techniques and development of microbial consortia, scale-up studies and in situ applications have been possible. In general, hydrocarbon uptake in this yeast is mediated by attachment to large droplets (via hydrophobic cell surfaces) or is aided by surfactants and emulsifiers. Subsequently, the internalized hydrocarbons are degraded by relevant enzymes innately present in the yeast. Some wild-type or recombinant strains also detoxify nitroaromatic (2,4,6-trinitrotoluene), halogenated (chlorinated and brominated hydrocarbons) and organophosphate (methyl parathion) compounds. The yeast can tolerate some metals and detoxify them via different biomolecules. The biomass (unmodified, in combination with sludge, magnetically-modified and in the biofilm form) has been employed in the biosorption of hexavalent chromium ions from aqueous solutions. Yeast cells have also been applied in protocols related to nanoparticle synthesis. The treatment of oily and solid wastes with this yeast reduces chemical oxygen demand or value-added products (single cell oil, single cell protein, surfactants, organic acids and polyalcohols) are obtained. On account of all these features, the microorganism has established a place for itself and is of considerable value in environment-related applications.
Collapse
Affiliation(s)
- Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India.
| | - Mugdha Apte
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India
| | - Pallavi Mohite
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India
| |
Collapse
|
42
|
Phosphatidic acid and phosphoinositides facilitate liposome association of Yas3p and potentiate derepression of ARE1 (alkane-responsive element one)-mediated transcription control. Fungal Genet Biol 2013; 61:100-10. [DOI: 10.1016/j.fgb.2013.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/18/2013] [Accepted: 09/28/2013] [Indexed: 11/18/2022]
|
43
|
Zinjarde SS. Food-related applications of Yarrowia lipolytica. Food Chem 2013; 152:1-10. [PMID: 24444899 DOI: 10.1016/j.foodchem.2013.11.117] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 01/01/2023]
Abstract
Yarrowia lipolytica is a non-pathogenic generally regarded as safe yeast. It displays unique physiological as well as biochemical properties that are relevant in food-related applications. Strains naturally associated with meat and dairy products contribute towards specific textures and flavours. On some occasions they cause food spoilage. They produce food-additives such as aroma compounds, organic acids, polyalcohols, emulsifiers and surfactants. The yeast biomass has been projected as single cell oil and single cell protein. Y. lipolytica degrades or upgrades different types of food wastes and in some cases, value-added products have also been obtained. The yeast is thus involved in the manufacture of food stuffs, making of food ingredients, generation of biomass that can be used as food or feed and in the effective treatment of food wastes. On account of all these features, this versatile yeast is of considerable significance in food-related applications.
Collapse
Affiliation(s)
- Smita S Zinjarde
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India.
| |
Collapse
|