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Leo P, de Melo Texeira M, Chander AM, Singh NK, Simpson AC, Yurkov A, Karouia F, Stajich JE, Mason CE, Venkateswaran K. Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities. IMA Fungus 2023; 14:15. [PMID: 37568226 PMCID: PMC10422843 DOI: 10.1186/s43008-023-00119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/20/2023] [Indexed: 08/13/2023] Open
Abstract
During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.
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Affiliation(s)
- Patrick Leo
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Mestre, Italy
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'università snc, 01100, Viterbo, Italy
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Marcus de Melo Texeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - Atul M Chander
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Nitin K Singh
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Anna C Simpson
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Fathi Karouia
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, PO BOX 1 MS 239/4, Moffett Field, CA, 94035, USA
- Space Research Within Reach, San Francisco, CA, 941110, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of CA-Riverside, Riverside, CA, 92521, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kasthuri Venkateswaran
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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Bijlani S, Parker C, Singh NK, Sierra MA, Foox J, Wang CCC, Mason CE, Venkateswaran K. Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi, the First Novel Eukaryote Isolated from the International Space Station. J Fungi (Basel) 2022; 8:165. [PMID: 35205919 PMCID: PMC8875396 DOI: 10.3390/jof8020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 12/25/2022] Open
Abstract
Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and 5% CO2 conditions. Confocal, scanning, and transmission electron microscopy revealed distinct morphological differences between the microgravity-grown cells and the standard Earth gravity-grown cells, including larger cells and thicker cell walls, altered intracellular morphology, modifications to extracellular fimbriae, budding, and the shedding of bud scars. Phylogenetic analyses via multi-locus sequence typing indicated that these ISS strains represented a single species in the genus Naganishia and were clustered with Naganishia diffluens. The name Naganishia tulchinskyi is proposed to accommodate these strains, with IF6SW-B1T as the holotype. The gene ontologies were assigned to the cell morphogenesis, microtubule-based response, and response to UV light, suggesting a variety of phenotypes that are well suited to respond to microgravity and radiation. Genomic analyses also indicated that the extracellular region, outer membrane, and cell wall were among the highest cellular component results, thus implying a set of genes associated with Titan-like cell plasticity. Finally, the highest molecular function matches included cytoskeletal motor activity, microtubule motor activity, and nuclear export signal receptor activity.
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Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Ceth Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Maria A. Sierra
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA;
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jonathan Foox
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Christopher E. Mason
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
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Dakal TC, Dhabhai B. Current status of genetic & metabolic engineering and novel QTL mapping-based strategic approach in bioethanol production. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ahmed El-Imam AM, Greetham D, Du C, Dyer PS. The development of a biorefining strategy for the production of biofuel from sorghum milling waste. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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The establishment of a marine focused biorefinery for bioethanol production using seawater and a novel marine yeast strain. Sci Rep 2018; 8:12127. [PMID: 30108287 PMCID: PMC6092365 DOI: 10.1038/s41598-018-30660-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/26/2018] [Indexed: 01/04/2023] Open
Abstract
Current technologies for bioethanol production rely on the use of freshwater for preparing the fermentation media and use yeasts of a terrestrial origin. Life cycle assessment has suggested that between 1,388 to 9,812 litres of freshwater are consumed for every litre of bioethanol produced. Hence, bioethanol is considered a product with a high-water footprint. This paper investigated the use of seawater-based media and a novel marine yeast strain ‘Saccharomyces cerevisiae AZ65’ to reduce the water footprint of bioethanol. Results revealed that S. cerevisiae AZ65 had a significantly higher osmotic tolerance when compared with the terrestrial reference strain. Using 15-L bioreactors, S. cerevisiae AZ65 produced 93.50 g/L ethanol with a yield of 83.33% (of the theoretical yield) and a maximum productivity of 2.49 g/L/h when using seawater-YPD media. This approach was successfully applied using an industrial fermentation substrate (sugarcane molasses). S. cerevisiae AZ65 produced 52.23 g/L ethanol using molasses media prepared in seawater with a yield of 73.80% (of the theoretical yield) and a maximum productivity of 1.43 g/L/h. These results demonstrated that seawater can substitute freshwater for bioethanol production without compromising production efficiency. Results also revealed that marine yeast is a potential candidate for use in the bioethanol industry especially when using seawater or high salt based fermentation media.
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Kawazoe N, Kimata Y, Izawa S. Acetic Acid Causes Endoplasmic Reticulum Stress and Induces the Unfolded Protein Response in Saccharomyces cerevisiae. Front Microbiol 2017; 8:1192. [PMID: 28702017 PMCID: PMC5487434 DOI: 10.3389/fmicb.2017.01192] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/12/2017] [Indexed: 02/02/2023] Open
Abstract
Since acetic acid inhibits the growth and fermentation ability of Saccharomyces cerevisiae, it is one of the practical hindrances to the efficient production of bioethanol from a lignocellulosic biomass. Although extensive information is available on yeast response to acetic acid stress, the involvement of endoplasmic reticulum (ER) and unfolded protein response (UPR) has not been addressed. We herein demonstrated that acetic acid causes ER stress and induces the UPR. The accumulation of misfolded proteins in the ER and activation of Ire1p and Hac1p, an ER-stress sensor and ER stress-responsive transcription factor, respectively, were induced by a treatment with acetic acid stress (>0.2% v/v). Other monocarboxylic acids such as propionic acid and sorbic acid, but not lactic acid, also induced the UPR. Additionally, ire1Δ and hac1Δ cells were more sensitive to acetic acid than wild-type cells, indicating that activation of the Ire1p-Hac1p pathway is required for maximum tolerance to acetic acid. Furthermore, the combination of mild acetic acid stress (0.1% acetic acid) and mild ethanol stress (5% ethanol) induced the UPR, whereas neither mild ethanol stress nor mild acetic acid stress individually activated Ire1p, suggesting that ER stress is easily induced in yeast cells during the fermentation process of lignocellulosic hydrolysates. It was possible to avoid the induction of ER stress caused by acetic acid and the combined stress by adjusting extracellular pH.
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Affiliation(s)
- Nozomi Kawazoe
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of TechnologyKyoto, Japan
| | - Yukio Kimata
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyNara, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of TechnologyKyoto, Japan
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Henriques SF, Mira NP, Sá-Correia I. Genome-wide search for candidate genes for yeast robustness improvement against formic acid reveals novel susceptibility (Trk1 and positive regulators) and resistance (Haa1-regulon) determinants. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:96. [PMID: 28428821 PMCID: PMC5395885 DOI: 10.1186/s13068-017-0781-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Formic acid is an inhibitory compound present in lignocellulosic hydrolysates. Understanding the complex molecular mechanisms underlying Saccharomyces cerevisiae tolerance to this weak acid at the system level is instrumental to guide synthetic pathway engineering for robustness improvement of industrial strains envisaging their use in lignocellulosic biorefineries. RESULTS This study was performed to identify, at a genome-wide scale, genes whose expression confers protection or susceptibility to formic acid, based on the screening of a haploid deletion mutant collection to search for these phenotypes in the presence of 60, 70 and 80 mM of this acid, at pH 4.5. This chemogenomic analysis allowed the identification of 172 determinants of tolerance and 41 determinants of susceptibility to formic acid. Clustering of genes required for maximal tolerance to this weak acid, based on their biological function, indicates an enrichment of those involved in intracellular trafficking and protein synthesis, cell wall and cytoskeleton organization, carbohydrate metabolism, lipid, amino acid and vitamin metabolism, response to stress, chromatin remodelling, transcription and internal pH homeostasis. Among these genes is HAA1 encoding the main transcriptional regulator of yeast transcriptome reprograming in response to acetic acid and genes of the Haa1-regulon; all demonstrated determinants of acetic acid tolerance. Among the genes that when deleted lead to increased tolerance to formic acid, TRK1, encoding the high-affinity potassium transporter and a determinant of resistance to acetic acid, was surprisingly found. Consistently, genes encoding positive regulators of Trk1 activity were also identified as formic acid susceptibility determinants, while a negative regulator confers protection. At a saturating K+ concentration of 20 mM, the deletion mutant trk1Δ was found to exhibit a much higher tolerance compared with the parental strain. Given that trk1Δ accumulates lower levels of radiolabelled formic acid, compared to the parental strain, it is hypothesized that Trk1 facilitates formic acid uptake into the yeast cell. CONCLUSIONS The list of genes resulting from this study shows a few marked differences from the list of genes conferring protection to acetic acid and provides potentially valuable information to guide improvement programmes for the development of more robust strains against formic acid.
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Affiliation(s)
- Sílvia F. Henriques
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Nuno P. Mira
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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8
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Global Transcriptomic Analysis of the Response of Corynebacterium glutamicum to Vanillin. PLoS One 2016; 11:e0164955. [PMID: 27760214 PMCID: PMC5070772 DOI: 10.1371/journal.pone.0164955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/04/2016] [Indexed: 12/01/2022] Open
Abstract
Lignocellulosic biomass is an abundant and renewable resource for biofuels and bio-based chemicals. Vanillin is one of the major phenolic inhibitors in biomass production using lignocellulose. To assess the response of Corynebacterium glutamicum to vanillin stress, we performed a global transcriptional response analysis. The transcriptional data showed that the vanillin stress not only affected the genes involved in degradation of vanillin, but also differentially regulated several genes related to the stress response, ribosome/translation, protein secretion, and the cell envelope. Moreover, deletion of the sigH or msrA gene in C. glutamicum resulted in a decrease in cell viability under vanillin stress. These insights will promote further engineering of model industrial strains, with enhanced tolerance or degradation ability to vanillin to enable suitable production of biofuels and bio-based chemicals from lignocellulosic biomass.
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García M, Greetham D, Wimalasena T, Phister T, Cabellos J, Arroyo T. The phenotypic characterization of yeast strains to stresses inherent to wine fermentation in warm climates. J Appl Microbiol 2016; 121:215-33. [DOI: 10.1111/jam.13139] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 02/05/2016] [Accepted: 03/11/2016] [Indexed: 11/30/2022]
Affiliation(s)
- M. García
- Departamento de Calidad Agroalimentaria; IMIDRA; Alcalá de Henares Spain
| | - D. Greetham
- Bioenergy & Brewing Science; School of Biosciences; University of Nottingham; Loughborough UK
| | - T.T. Wimalasena
- Bioenergy & Brewing Science; School of Biosciences; University of Nottingham; Loughborough UK
| | | | - J.M. Cabellos
- Departamento de Calidad Agroalimentaria; IMIDRA; Alcalá de Henares Spain
| | - T. Arroyo
- Departamento de Calidad Agroalimentaria; IMIDRA; Alcalá de Henares Spain
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Lima MS, Damasio ARDL, Crnkovic PM, Pinto MR, da Silva AM, da Silva JCR, Segato F, de Lucas RC, Jorge JA, Polizeli MDLTDM. Co-cultivation of Aspergillus nidulans Recombinant Strains Produces an Enzymatic Cocktail as Alternative to Alkaline Sugarcane Bagasse Pretreatment. Front Microbiol 2016; 7:583. [PMID: 27199917 PMCID: PMC4848300 DOI: 10.3389/fmicb.2016.00583] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Plant materials represent a strategic energy source because they can give rise to sustainable biofuels through the fermentation of their carbohydrates. A clear example of a plant-derived biofuel resource is the sugar cane bagasse exhibiting 60-80% of fermentable sugars in its composition. However, the current methods of plant bioconversion employ severe and harmful chemical/physical pretreatments raising biofuel cost production and environmental degradation. Replacing these methods with co-cultivated enzymatic cocktails is an alternative. Here we propose a pretreatment for sugarcane bagasse using a multi-enzymatic cocktail from the co-cultivation of four Aspergillus nidulans recombinant strains. The co-cultivation resulted in the simultaneous production of GH51 arabinofuranosidase (AbfA), GH11 endo-1,4-xylanase (XlnA), GH43 endo-1,5-arabinanase (AbnA) and GH12 xyloglucan specific endo-β-1,4-glucanase (XegA). This core set of recombinant enzymes was more efficient than the alternative alkaline method in maintaining the cellulose integrity and exposing this cellulose to the following saccharification process. Thermogravimetric and differential thermal analysis revealed residual byproducts on the alkali pretreated biomass, which were not found in the enzymatic pretreatment. Therefore, the enzymatic pretreatment was residue-free and seemed to be more efficient than the applied alkaline method, which makes it suitable for bioethanol production.
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Affiliation(s)
- Matheus S Lima
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo São Paulo, Brazil
| | - André R de L Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas São Paulo, Brazil
| | - Paula M Crnkovic
- Department of Mechanical Engineering, University of São Paulo São Paulo, Brazil
| | - Marcelo R Pinto
- Laboratory of Biopathology and Molecular Biology, Uberaba University Uberaba, Brazil
| | | | - Jean C R da Silva
- Federal Institute of Education, Science and Technology of São Paulo São Paulo, Brazil
| | - Fernando Segato
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo São Paulo, Brazil
| | - Rosymar C de Lucas
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São PauloSão Paulo, Brazil; Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São PauloSão Paulo, Brazil
| | - João A Jorge
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo São Paulo, Brazil
| | - Maria de L T de M Polizeli
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo São Paulo, Brazil
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Kostas ET, White DA, Du C, Cook DJ. Selection of yeast strains for bioethanol production from UK seaweeds. JOURNAL OF APPLIED PHYCOLOGY 2016; 28:1427-1441. [PMID: 27057090 PMCID: PMC4789230 DOI: 10.1007/s10811-015-0633-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 05/24/2015] [Accepted: 05/24/2015] [Indexed: 05/13/2023]
Abstract
Macroalgae (seaweeds) are a promising feedstock for the production of third generation bioethanol, since they have high carbohydrate contents, contain little or no lignin and are available in abundance. However, seaweeds typically contain a more diverse array of monomeric sugars than are commonly present in feedstocks derived from lignocellulosic material which are currently used for bioethanol production. Hence, identification of a suitable fermentative microorganism that can utilise the principal sugars released from the hydrolysis of macroalgae remains a major objective. The present study used a phenotypic microarray technique to screen 24 different yeast strains for their ability to metabolise individual monosaccharides commonly found in seaweeds, as well as hydrolysates following an acid pre-treatment of five native UK seaweed species (Laminaria digitata, Fucus serratus, Chondrus crispus, Palmaria palmata and Ulva lactuca). Five strains of yeast (three Saccharomyces spp, one Pichia sp and one Candida sp) were selected and subsequently evaluated for bioethanol production during fermentation of the hydrolysates. Four out of the five selected strains converted these monomeric sugars into bioethanol, with the highest ethanol yield (13 g L-1) resulting from a fermentation using C. crispus hydrolysate with Saccharomyces cerevisiae YPS128. This study demonstrated the novel application of a phenotypic microarray technique to screen for yeast capable of metabolising sugars present in seaweed hydrolysates; however, metabolic activity did not always imply fermentative production of ethanol.
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Affiliation(s)
- Emily T. Kostas
- />The University of Nottingham, Sutton Bonington Campus, Bioenergy and Brewing Science Building, Loughborough, Leicestershire LE12 5RD UK
| | - Daniel A. White
- />Plymouth Marine Laboratory, Prospect Pl, Plymouth, Devon PL1 3DH UK
| | - Chenyu Du
- />The University of Nottingham, Sutton Bonington Campus, Bioenergy and Brewing Science Building, Loughborough, Leicestershire LE12 5RD UK
| | - David J. Cook
- />The University of Nottingham, Sutton Bonington Campus, Bioenergy and Brewing Science Building, Loughborough, Leicestershire LE12 5RD UK
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Nguyen TTM, Iwaki A, Izawa S. The ADH7 Promoter of Saccharomyces cerevisiae is Vanillin-Inducible and Enables mRNA Translation Under Severe Vanillin Stress. Front Microbiol 2015; 6:1390. [PMID: 26696995 PMCID: PMC4676198 DOI: 10.3389/fmicb.2015.01390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 12/24/2022] Open
Abstract
Vanillin is one of the major phenolic aldehyde compounds derived from lignocellulosic biomass and acts as a potent fermentation inhibitor to repress the growth and fermentative ability of yeast. Vanillin can be reduced to its less toxic form, vanillyl alcohol, by the yeast NADPH-dependent medium chain alcohol dehydrogenases, Adh6 and Adh7. However, there is little information available regarding the regulation of their gene expression upon severe vanillin stress, which has been shown to repress the bulk translation activity in yeast cells. Therefore, in this study, we investigated expression patterns of the ADH6 and ADH7 genes in the presence of high concentrations of vanillin. We found that although both genes were transcriptionally upregulated by vanillin stress, they showed different protein expression patterns in response to vanillin. Expression of Adh6 was constitutive and gradually decreased under vanillin stress, whereas expression of Adh7 was inducible, and, importantly, occurred under severe vanillin stress. The null mutants of ADH6 or ADH7 genes were hypersensitive to vanillin and reduced vanillin less efficiently than the wild type, confirming the importance of Adh6 and Adh7 in vanillin detoxification. Additionally, we demonstrate that the ADH7 promoter is vanillin-inducible and enables effective protein synthesis even under severe vanillin stress, and it may be useful for the improvement of vanillin-tolerance and biofuel production efficiency via modification of yeast gene expression in the presence of high concentrations of vanillin.
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Affiliation(s)
- Trinh T M Nguyen
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
| | - Aya Iwaki
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
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Kumar V, Hart AJ, Keerthiraju ER, Waldron PR, Tucker GA, Greetham D. Expression of Mitochondrial Cytochrome C Oxidase Chaperone Gene (COX20) Improves Tolerance to Weak Acid and Oxidative Stress during Yeast Fermentation. PLoS One 2015; 10:e0139129. [PMID: 26427054 PMCID: PMC4591339 DOI: 10.1371/journal.pone.0139129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/08/2015] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Saccharomyces cerevisiae is the micro-organism of choice for the conversion of fermentable sugars released by the pre-treatment of lignocellulosic material into bioethanol. Pre-treatment of lignocellulosic material releases acetic acid and previous work identified a cytochrome oxidase chaperone gene (COX20) which was significantly up-regulated in yeast cells in the presence of acetic acid. RESULTS A Δcox20 strain was sensitive to the presence of acetic acid compared with the background strain. Overexpressing COX20 using a tetracycline-regulatable expression vector system in a Δcox20 strain, resulted in tolerance to the presence of acetic acid and tolerance could be ablated with addition of tetracycline. Assays also revealed that overexpression improved tolerance to the presence of hydrogen peroxide-induced oxidative stress. CONCLUSION This is a study which has utilised tetracycline-regulated protein expression in a fermentation system, which was characterised by improved (or enhanced) tolerance to acetic acid and oxidative stress.
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Affiliation(s)
- Vinod Kumar
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Andrew J. Hart
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Ethiraju R. Keerthiraju
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Paul R. Waldron
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Gregory A. Tucker
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Darren Greetham
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
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Oshoma CE, Greetham D, Louis EJ, Smart KA, Phister TG, Powell C, Du C. Screening of Non- Saccharomyces cerevisiae Strains for Tolerance to Formic Acid in Bioethanol Fermentation. PLoS One 2015; 10:e0135626. [PMID: 26284784 PMCID: PMC4540574 DOI: 10.1371/journal.pone.0135626] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/24/2015] [Indexed: 11/18/2022] Open
Abstract
Formic acid is one of the major inhibitory compounds present in hydrolysates derived from lignocellulosic materials, the presence of which can significantly hamper the efficiency of converting available sugars into bioethanol. This study investigated the potential for screening formic acid tolerance in non-Saccharomyces cerevisiae yeast strains, which could be used for the development of advanced generation bioethanol processes. Spot plate and phenotypic microarray methods were used to screen the formic acid tolerance of 7 non-Saccharomyces cerevisiae yeasts. S. kudriavzeii IFO1802 and S. arboricolus 2.3319 displayed a higher formic acid tolerance when compared to other strains in the study. Strain S. arboricolus 2.3319 was selected for further investigation due to its genetic variability among the Saccharomyces species as related to Saccharomyces cerevisiae and availability of two sibling strains: S. arboricolus 2.3317 and 2.3318 in the lab. The tolerance of S. arboricolus strains (2.3317, 2.3318 and 2.3319) to formic acid was further investigated by lab-scale fermentation analysis, and compared with S. cerevisiae NCYC2592. S. arboricolus 2.3319 demonstrated improved formic acid tolerance and a similar bioethanol synthesis capacity to S. cerevisiae NCYC2592, while S. arboricolus 2.3317 and 2.3318 exhibited an overall inferior performance. Metabolite analysis indicated that S. arboricolus strain 2.3319 accumulated comparatively high concentrations of glycerol and glycogen, which may have contributed to its ability to tolerate high levels of formic acid.
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Affiliation(s)
- Cyprian E. Oshoma
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
| | - Darren Greetham
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
| | - Edward J. Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | | | - Trevor G. Phister
- PepsiCo Int. Beaumont Park, Leycroft Road, Leicester, United Kingdom
| | - Chris Powell
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
| | - Chenyu Du
- Bioenergy and Brewing Science Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, United Kingdom
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
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Acetylcholine Protects against Candida albicans Infection by Inhibiting Biofilm Formation and Promoting Hemocyte Function in a Galleria mellonella Infection Model. EUKARYOTIC CELL 2015; 14:834-44. [PMID: 26092919 DOI: 10.1128/ec.00067-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/15/2015] [Indexed: 11/20/2022]
Abstract
Both neuronal acetylcholine and nonneuronal acetylcholine have been demonstrated to modulate inflammatory responses. Studies investigating the role of acetylcholine in the pathogenesis of bacterial infections have revealed contradictory findings with regard to disease outcome. At present, the role of acetylcholine in the pathogenesis of fungal infections is unknown. Therefore, the aim of this study was to determine whether acetylcholine plays a role in fungal biofilm formation and the pathogenesis of Candida albicans infection. The effect of acetylcholine on C. albicans biofilm formation and metabolism in vitro was assessed using a crystal violet assay and phenotypic microarray analysis. Its effect on the outcome of a C. albicans infection, fungal burden, and biofilm formation were investigated in vivo using a Galleria mellonella infection model. In addition, its effect on modulation of host immunity to C. albicans infection was also determined in vivo using hemocyte counts, cytospin analysis, larval histology, lysozyme assays, hemolytic assays, and real-time PCR. Acetylcholine was shown to have the ability to inhibit C. albicans biofilm formation in vitro and in vivo. In addition, acetylcholine protected G. mellonella larvae from C. albicans infection mortality. The in vivo protection occurred through acetylcholine enhancing the function of hemocytes while at the same time inhibiting C. albicans biofilm formation. Furthermore, acetylcholine also inhibited inflammation-induced damage to internal organs. This is the first demonstration of a role for acetylcholine in protection against fungal infections, in addition to being the first report that this molecule can inhibit C. albicans biofilm formation. Therefore, acetylcholine has the capacity to modulate complex host-fungal interactions and plays a role in dictating the pathogenesis of fungal infections.
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Kumar V, Hart AJ, Wimalasena TT, Tucker GA, Greetham D. Expression of RCK2 MAPKAP (MAPK-activated protein kinase) rescues yeast cells sensitivity to osmotic stress. Microb Cell Fact 2015; 14:85. [PMID: 26062605 PMCID: PMC4464721 DOI: 10.1186/s12934-015-0276-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 11/20/2022] Open
Abstract
Background Saccharomyces cerevisiae is the micro-organism of choice for the conversion of fermentable sugars during beverage or bioethanol fermentations. These fermentations are characterised by high osmotic stress on a yeast cell, with selected brewing fermentations beginning at 20–25% fermentable sugars and bioethanol fermentations at 13% fermentable sugars. Results RCK2 encodes for a MAPKAP (MAPK-activated protein kinase) enzyme and was identified on a locus by QTL analysis in yeast cells under osmotic stress, RCK2 expression was placed under a tetracycline regulatable vector and rescued glucose, sorbitol or glycerol induced osmotic stress in an rck2 null strain. A strain overexpressing RCK2 had significantly faster fermentation rates when compared with the empty vector control strain. Conclusions Presence of RCK2 increased rates of glucose utilisation (~40 g glucose in first 8 h) during a 15% glucose fermentation and concurrent production of ethanol when compared with empty vector controls. Tolerance to osmotic stress using the tetracycline regulatable vectors could be turned off with the addition of tetracycline returning a rck2 null strain back to osmotic sensitivity. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0276-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V Kumar
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Nottingham, LE12 5RD, UK.
| | - A J Hart
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Nottingham, LE12 5RD, UK.
| | - T T Wimalasena
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Nottingham, LE12 5RD, UK. .,Kingston Research Ltd, SaltEnd Chemicals Park, Hull, UK.
| | - G A Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Nottingham, LE12 5RD, UK.
| | - D Greetham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Nottingham, LE12 5RD, UK.
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Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y. Detoxification of 5-hydroxymethylfurfural by the Pleurotus ostreatus lignolytic enzymes aryl alcohol oxidase and dehydrogenase. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:63. [PMID: 25897324 PMCID: PMC4403834 DOI: 10.1186/s13068-015-0244-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/24/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Current large-scale pretreatment processes for lignocellulosic biomass are generally accompanied by the formation of toxic degradation products, such as 5-hydroxymethylfurfural (HMF), which inhibit cellulolytic enzymes and fermentation by ethanol-producing yeast. Overcoming these toxic effects is a key technical barrier in the biochemical conversion of plant biomass to biofuels. Pleurotus ostreatus, a white-rot fungus, can efficiently degrade lignocellulose. In this study, we analyzed the ability of P. ostreatus to tolerate and metabolize HMF and investigated relevant molecular pathways associated with these processes. RESULTS P. ostreatus was capable to metabolize and detoxify HMF 30 mM within 48 h, converting it into 2,5-bis-hydroxymethylfuran (HMF alcohol) and 2,5-furandicarboxylic acid (FDCA), which subsequently allowed the normal yeast growth in amended media. We show that two enzymes groups, which belong to the ligninolytic system, aryl-alcohol oxidases and a dehydrogenase, are involved in this process. HMF induced the transcription and production of these enzymes and was accompanied by an increase in activity levels. We also demonstrate that following the induction of these enzymes, HMF could be metabolized in vitro. CONCLUSIONS Aryl-alcohol oxidase and dehydrogenase gene family members are part of the transcriptional and subsequent translational response to HMF exposure in P. ostreatus and are involved in HMF transformation. Based on our data, we propose that these enzymatic capacities of P. ostreatus either be integrated in biomass pretreatment or the genes encoding these enzymes may function to detoxify HMF via heterologous expression in fermentation organisms, such as Saccharomyces cerevisiae.
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Affiliation(s)
- Daria Feldman
- />Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot, 76100 Israel
| | - David J Kowbel
- />Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, California 94720 USA
| | - N Louise Glass
- />Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, California 94720 USA
| | - Oded Yarden
- />Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot, 76100 Israel
| | - Yitzhak Hadar
- />Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot, 76100 Israel
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Assessing the potential of wild yeasts for bioethanol production. J Ind Microbiol Biotechnol 2014; 42:39-48. [PMID: 25413210 DOI: 10.1007/s10295-014-1544-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
Bioethanol fermentations expose yeasts to a new, complex and challenging fermentation medium with specific inhibitors and sugar mixtures depending on the type of carbon source. It is, therefore, suggested that the natural diversity of yeasts should be further exploited in order to find yeasts with good ethanol yield in stressed fermentation media. In this study, we screened more than 50 yeast isolates of which we selected five isolates with promising features. The species Candida bombi, Wickerhamomyces anomalus and Torulaspora delbrueckii showed better osmo- and hydroxymethylfurfural tolerance than Saccharomyces cerevisiae. However, S. cerevisiae isolates had the highest ethanol yield in fermentation experiments mimicking high gravity fermentations (25 % glucose) and artificial lignocellulose hydrolysates (with a myriad of inhibitors). Interestingly, among two tested S. cerevisiae strains, a wild strain isolated from an oak tree performed better than Ethanol Red, a S. cerevisiae strain which is currently commonly used in industrial bioethanol fermentations. Additionally, a W. anomalus strain isolated from sugar beet thick juice was found to have a comparable ethanol yield, but needed longer fermentation time. Other non-Saccharomyces yeasts yielded lower ethanol amounts.
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