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Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 2018. [DOI: 10.1093/femsre/fuy009] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 1, SI-1000 Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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Harding T, Roger AJ, Simpson AGB. Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers. Front Microbiol 2017; 8:944. [PMID: 28611746 PMCID: PMC5447177 DOI: 10.3389/fmicb.2017.00944] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa. To gather fundamental knowledge about salt adaptation in these organisms, we studied the transcriptome-level response of Halocafeteria seosinensis (Stramenopiles) grown under contrasting salinities. We provided further evolutionary context to our analysis by identifying genes that underwent recent duplications. Genes that were highly responsive to salinity variations were involved in stress response (e.g., chaperones), ion homeostasis (e.g., Na+/H+ transporter), metabolism and transport of lipids (e.g., sterol biosynthetic genes), carbohydrate metabolism (e.g., glycosidases), and signal transduction pathways (e.g., transcription factors). A significantly high proportion (43%) of duplicated genes were also differentially expressed, accentuating the importance of gene expansion in adaptation by H. seosinensis to high salt environments. Furthermore, we found two genes that were lateral acquisitions from bacteria, and were also highly up-regulated and highly expressed at high salt, suggesting that this evolutionary mechanism could also have facilitated adaptation to high salt. We propose that a transition toward high-salt adaptation in the ancestors of H. seosinensis required the acquisition of new genes via duplication, and some lateral gene transfers (LGTs), as well as the alteration of transcriptional programs, leading to increased stress resistance, proper establishment of ion gradients, and modification of cell structure properties like membrane fluidity.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
| | - Alastair G. B. Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
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Yaguchi A, Rives D, Blenner M. New kids on the block: emerging oleaginous yeast of biotechnological importance. AIMS Microbiol 2017; 3:227-247. [PMID: 31294158 PMCID: PMC6605006 DOI: 10.3934/microbiol.2017.2.227] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 03/23/2017] [Indexed: 12/24/2022] Open
Abstract
There is growing interest in using oleaginous yeast for the production of a variety of fatty acids and fatty acid-derived oleochemicals. This is motivated by natural propensity for high flux through lipid biosynthesis that has naturally evolved, making them a logical starting point for additional genetic engineering to improve titers and productivities. Much of the academic and industrial focus has centered on yeast that have significant genetic engineering tool capabilities, such as Yarrowia lipolytica, and those that have naturally high lipid accumulation, such as Rhodosporidium toruloides and Lipomyces starkeyi; however, there are oleaginous yeast with phenotypes better aligned with typically inhibitory process conditions, such as high salt concentrations and lignocellulosic derived inhibitors. This review addresses the foundational work in characterizing two emerging oleaginous yeast of interest: Debaryomyces hansenii and Trichosporon oleaginosus. We focus on the physiological and metabolic properties of these yeast that make each attractive for bioprocessing of lignocellulose to fuels and chemicals, discuss their respective genetic engineering tools and highlight the critical barriers facing the broader implementation of these oleaginous yeast.
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Affiliation(s)
- Allison Yaguchi
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC 29634, USA
| | - Dyllan Rives
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC 29634, USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC 29634, USA
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Response of Kluyveromyces lactis to Sodium Chloride Salt Stress and the Possibility of Enhanced Lipids Production. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.1.69] [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] Open
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Gunde-Cimerman N, Ramos J, Plemenitaš A. Halotolerant and halophilic fungi. ACTA ACUST UNITED AC 2009; 113:1231-41. [DOI: 10.1016/j.mycres.2009.09.002] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 09/02/2009] [Indexed: 11/30/2022]
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Turk M, Montiel V, Žigon D, Plemenitaš A, Ramos J. Plasma membrane composition of Debaryomyces hansenii adapts to changes in pH and external salinity. Microbiology (Reading) 2007; 153:3586-3592. [PMID: 17906155 DOI: 10.1099/mic.0.2007/009563-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Debaryomyces hansenii is a marine yeast that has to cope with different stress situations. Since changes in membrane properties can play an important function in adaptation, we have examined the fluidity and lipid composition of purified plasma membranes of D. hansenii grown at different external pH values and salt concentrations. Growth at low pH caused an increase in the sterol-to-phospholipid ratio and a decrease in fatty acid unsaturation which was reflected in decreased fluidity of the plasma membrane. High levels of NaCl increased the sterol-to-phospholipid ratio and fatty acid unsaturation, but did not significantly affect fluidity. The sterol-to-phospholipid ratios obtained in D. hansenii grown under any of these conditions were similar to the ratios that have been reported for halophilic/halotolerant black yeasts, but much smaller than those observed in the model yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Martina Turk
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, Ljubljana, Slovenia
| | - Vera Montiel
- Department of Microbiology, ETSIAM, Edificio Severo Ochoa, Campus de Rabanales, University of Cordoba, Spain
| | - Dušan Žigon
- J. Stefan Institute, Jamova 39, Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia
| | - José Ramos
- Department of Microbiology, ETSIAM, Edificio Severo Ochoa, Campus de Rabanales, University of Cordoba, Spain
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Breuer U, Harms H. Debaryomyces hansenii — an extremophilic yeast with biotechnological potential. Yeast 2006; 23:415-37. [PMID: 16652409 DOI: 10.1002/yea.1374] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We illuminate the ecological, physiological and genetic characteristics of the yeast Debaryomyces hansenii in the view of our belief that this metabolically versatile, non-pathogenic, osmotolerant and oleaginous microorganism represents an attractive target for fundamental and applied biotechnological research. To this end, we give a broad overview of extant biotechnological procedures using D. hansenii, e.g. in the manufacture of various foods, and propose research into the heterologous synthesis of a range of fine chemicals.
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Affiliation(s)
- Uta Breuer
- UFZ-Centre of Environmental Research Leipzig-Halle, Department of Environmental Microbiology, Permoserstrasse 15, D-04318 Leipzig, Germany.
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Turk M, Méjanelle L, Sentjurc M, Grimalt JO, Gunde-Cimerman N, Plemenitas A. Salt-induced changes in lipid composition and membrane fluidity of halophilic yeast-like melanized fungi. Extremophiles 2003; 8:53-61. [PMID: 15064990 DOI: 10.1007/s00792-003-0360-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2002] [Accepted: 09/12/2003] [Indexed: 11/28/2022]
Abstract
The halophilic melanized yeast-like fungi Hortaea werneckii, Phaeotheca triangularis, and the halotolerant Aureobasidium pullulans, isolated from salterns as their natural environment, were grown at different NaCl concentrations and their membrane lipid composition and fluidity were examined. Among sterols, besides ergosterol, which was the predominant one, 23 additional sterols were identified. Their total content did not change consistently or significantly in response to raised NaCl concentrations in studied melanized fungi. The major phospholipid classes were phosphatidylcholine and phosphatidylethanolamine, followed by anionic phospholipids. The most abundant fatty acids in phospholipids contained C16 and C18 chain lengths with a high percentage of C18:2Delta9,12. Salt stress caused an increase in the fatty acid unsaturation in the halophilic H. werneckii and halotolerant A. pullulans but a slight decrease in halophilic P. triangularis. All the halophilic fungi maintained their sterol-to-phospholipid ratio at a significantly lower level than did the salt-sensitive Saccharomyces cerevisiae and halotolerant A. pullulans. Electron paramagnetic resonance (EPR) spectroscopy measurements showed that the membranes of all halophilic fungi were more fluid than those of the halotolerant A. pullulans and salt-sensitive S. cerevisiae, which is in good agreement with the lipid composition observed in this study.
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Affiliation(s)
- Martina Turk
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia
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Oliveira R, Lages F, Silva-Graça M, Lucas C. Fps1p channel is the mediator of the major part of glycerol passive diffusion in Saccharomyces cerevisiae: artefacts and re-definitions. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1613:57-71. [PMID: 12832087 DOI: 10.1016/s0005-2736(03)00138-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Glycerol has been shown to cross the plasma membrane of Saccharomyces cerevisiae through (1) a H(+)/symport detected in cells grown on non-fermentable carbon sources, (2) the constitutively expressed Fps1p channel and (3) by passive diffusion. The Fps1p channel has been named a facilitator for mediating glycerol low affinity transport of the facilitated diffusion type. We present experimental evidence that this kinetic is an artefact created by glycerol kinase activity. Instead, the channel is shown to mediate the major part of glycerol's passive diffusion. This is not incompatible with Fps1p's major role in vivo, which has been previously shown to be the control of glycerol export under osmotic stress or in reaction to turgor changes. We also verified that FPS1 overexpression caused an increase in H(+)/symport V(max). Furthermore, yfl054c and fps1 mutants were equally affected by exogenously added ethanol, being the correspondent passive diffusion stimulated. For the first time, to our knowledge, a phenotype attributed to the functioning of YFL054c gene is presented. Glycerol passive diffusion is thus apparently channel-mediated. This is discussed according to glycerol's chemical properties, which contradict the widely spread concept of glycerol's liposoluble nature. The discussion considers the multiple roles that the intracellular levels of glycerol and its pathway regulation might play as a central key to metabolism control.
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Affiliation(s)
- Rui Oliveira
- Centro de Biologia da Universidade do Minho (CB-UM)/Departamento de Biologia, Campus de Gualtar, 4710-057 Braga, Portugal
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Sharma SC, Raj D, Forouzandeh M, Bansal MP. Salt-induced changes in lipid composition and ethanol tolerance in Saccharomyces cerevisiae. Appl Biochem Biotechnol 1996; 56:189-95. [PMID: 9045598 DOI: 10.1007/bf02786949] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The effect of salt stress on lipid composition and its relationship with ethanol tolerance in Saccharomyces cerevisiae was studied. Amounts of phospholipids as well as that of sterols decreased, whereas that of protein and glycolipids increased with increasing salt concentration. Relative proportion of amino phospholipids (phosphatidylethanolamine and phosphatidylserine) decreased, whereas that of phosphatidylcholine showed a reverse trend. Cells grown under increasing salt concentration were more resistant to ethanol-induced leakage of UV-absorbing substances, an index of ethanol endurance. Results showed an overlap between osmotolerance and ethanol tolerance in this strain.
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Affiliation(s)
- S C Sharma
- Department of Biochemistry, Panjab University Chandigarh, India
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Affiliation(s)
- A Blomberg
- Department of General and Marine Microbiology, University of Göteborg, Sweden
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Pilkington BJ, Rose AH. Incorporation of unsaturated fatty acids by Saccharomyces cerevisiae: conservation of fatty-acyl saturation in phosphatidylinositol. Yeast 1991; 7:489-94. [PMID: 1897314 DOI: 10.1002/yea.320070508] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Saccharomyces cerevisiae was grown anaerobically in media supplemented with myristoleic 14:1(9c), palmitoleic 16:1(9c), oleic 18:1(9c), linoleic 18:2(9,12c), gamma-linolenic 18:3(9,12,15c) or eicosenoic 20:1(11c) acid. Cells from exponential-phase cultures contained approximately the same proportions of the major phospholipid classes, namely phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylserine, the greatest differences being detected in cells grown in the presence of 14:1(9c) or 20:1(11c) acids. The extent to which phospholipids from cells were enriched with residues of the exogenously supplied acid varied from 52% in cells grown in the presence of 14:1(9c) acid to 13% in cells grown in media supplemented with 20:1(11c) acid. Analysis of the fatty-acyl composition of the four major phospholipid classes revealed that the degree of unsaturation varied considerably in three of the classes, while phosphatidylinositol conserved a high degree of saturation. The possible significance of the latter finding in relation to the physiological role of phosphatidylinositol in the plasma membrane is discussed.
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Affiliation(s)
- B J Pilkington
- Zymology Laboratory, School of Biological Sciences, Bath University, Avon, U.K
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Russell NJ. Adaptive modifications in membranes of halotolerant and halophilic microorganisms. J Bioenerg Biomembr 1989; 21:93-113. [PMID: 2651429 DOI: 10.1007/bf00762214] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Halotolerant and halophilic microorganisms can grow in (hyper)saline environments, but only halophiles specifically require salt. Genotypic and phenotypic adaptations are displayed by halophiles; the halotolerants adapt phenotypically, but it is not established whether they show genotypic adaptation. This paper reviews the various strategies of haloadaptation of membrane proteins and lipids by halotolerant and halophilic microorganisms. Moderate halophiles and halotolerants adapt their membrane lipid composition by increasing the proportion of anionic lipids, often phosphatidylglycerol and/or glycolipids, which in the moderately halophilic bacterium Vibrio costicola appears to be part of an osmoregulatory response to minimize membrane stress at high salinities. Extreme halophiles possess typical archaebacterial ether lipids, which are genotypically adapted by having additional substitutions with negatively-charged residues such as sulfate. In contrast to the lipids, it is less clear whether membrane proteins are haloadapted, although they may be more acidic; very few depend on salt for their activity.
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Affiliation(s)
- N J Russell
- Department of Biochemistry, University of Wales, Cardiff, U.K
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