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Barros KO, Mader M, Krause DJ, Pangilinan J, Andreopoulos B, Lipzen A, Mondo SJ, Grigoriev IV, Rosa CA, Sato TK, Hittinger CT. Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:20. [PMID: 38321504 PMCID: PMC10848558 DOI: 10.1186/s13068-024-02467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/28/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Cost-effective production of biofuels from lignocellulose requires the fermentation of D-xylose. Many yeast species within and closely related to the genera Spathaspora and Scheffersomyces (both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD+ to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. RESULTS We screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressed XYL genes from multiple Scheffersomyces species in a strain of Saccharomyces cerevisiae. Recombinant S. cerevisiae expressing XYL1 from Scheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared to S. cerevisiae strain expressing XYL genes from Scheffersomyces stipitis. CONCLUSION Collectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeast Sc. xylosifermentans as a potential source for genes that can be engineered into S. cerevisiae to improve xylose fermentation and biofuel production.
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Affiliation(s)
- Katharina O Barros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Megan Mader
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Krause
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Computer Science, San Jose State University, One Washington Square, San Jose, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Department, University of California Berkeley, Berkeley, CA, USA
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
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Bolzico BC, Racca S, Khawam JN, Leonardi RJ, Tomassi AH, Benzzo MT, Comelli RN. Exploring xylose metabolism in non-conventional yeasts: kinetic characterization and product accumulation under different aeration conditions. J Ind Microbiol Biotechnol 2024; 51:kuae023. [PMID: 38936832 PMCID: PMC11247345 DOI: 10.1093/jimb/kuae023] [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: 04/15/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
d-Xylose is a metabolizable carbon source for several non-Saccharomyces species, but not for native strains of S. cerevisiae. For the potential application of xylose-assimilating yeasts in biotechnological processes, a deeper understanding of pentose catabolism is needed. This work aimed to investigate the traits behind xylose utilization in diverse yeast species. The performance of 9 selected xylose-metabolizing yeast strains was evaluated and compared across 3 oxygenation conditions. Oxygenation diversely impacted growth, xylose consumption, and product accumulation. Xylose utilization by ethanol-producing species such as Spathaspora passalidarum and Scheffersomyces stipitis was less affected by oxygen restriction compared with other xylitol-accumulating species such as Meyerozyma guilliermondii, Naganishia liquefaciens, and Yamadazyma sp., for which increased aeration stimulated xylose assimilation considerably. Spathaspora passalidarum exhibited superior conversion of xylose to ethanol and showed the fastest growth and xylose consumption in all 3 conditions. By performing assays under identical conditions for all selected yeasts, we minimize bias in comparisons, providing valuable insight into xylose metabolism and facilitating the development of robust bioprocesses. ONE-SENTENCE SUMMARY This work aims to expand the knowledge of xylose utilization in different yeast species, with a focus on how oxygenation impacts xylose assimilation.
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Affiliation(s)
- Bruna C Bolzico
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Sofia Racca
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Jorge N Khawam
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Rodrigo J Leonardi
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Ariel H Tomassi
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Maria T Benzzo
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
| | - Raul N Comelli
- Grupo de Procesos Biológicos en Ingeniería Ambiental (GPBIA), Facultad de Ingeniería y Ciencias Hídricas (FICH), Universidad Nacional del Litoral (UNL), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, CC 242 Paraje El Pozo, Santa Fe 3000, Argentina
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Albuini FM, de Castro AG, Campos VJ, Ribeiro LE, Vidigal PMP, de Oliveira Mendes TA, Fietto LG. Transcriptome profiling brings new insights into the ethanol stress responses of Spathaspora passalidarum. Appl Microbiol Biotechnol 2023; 107:6573-6589. [PMID: 37658163 DOI: 10.1007/s00253-023-12730-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
Spathaspora passalidarum is a xylose-fermenting microorganism promising for the fermentation of lignocellulosic hydrolysates. This yeast is more sensitive to ethanol than Saccharomyces cerevisiae for unclear reasons. An RNA-seq experiment was performed to identify transcriptional changes in S. passalidarum in response to ethanol and gain insights into this phenotype. The results showed the upregulation of genes associated with translation and the downregulation of genes encoding proteins involved in lipid metabolism, transporters, and enzymes from glycolysis and fermentation pathways. Our results also revealed that genes encoding heat-shock proteins and involved in antioxidant response were upregulated, whereas the osmotic stress response of S. passalidarum appears impaired under ethanol stress. A pseudohyphal morphology of S. passalidarum colonies was observed in response to ethanol stress, which suggests that ethanol induces a misperception of nitrogen availability in the environment. Changes in the yeast fatty acid profile were observed only after 12 h of ethanol exposure, coinciding with the recovery of the yeast xylose consumption ability. These findings suggest that the lack of fast membrane lipid adjustments, the halt in nutrient absorption and cellular metabolism, and the failure to induce the expression of osmotic stress-responsive genes are the main aspects underlying the low ethanol tolerance of S. passalidarum. KEY POINTS: • Ethanol stress halts Spathaspora passalidarum metabolism and fermentation • Genes encoding nutrient transporters showed downregulation under ethanol stress • Ethanol induces a pseudohyphal cell shape, suggesting a misperception of nutrients.
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Affiliation(s)
- Fernanda Matias Albuini
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Alex Gazolla de Castro
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Valquíria Júnia Campos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Lílian Emídio Ribeiro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Luciano Gomes Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil.
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Alencar BRA, de Freitas RAA, Guimarães VEP, Silva RK, Elsztein C, da Silva SP, Dutra ED, de Morais Junior MA, de Souza RB. Meyerozyma caribbica Isolated from Vinasse-Irrigated Sugarcane Plantation Soil: A Promising Yeast for Ethanol and Xylitol Production in Biorefineries. J Fungi (Basel) 2023; 9:789. [PMID: 37623560 PMCID: PMC10455855 DOI: 10.3390/jof9080789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
The production of fuels and other industrial products from renewable sources has intensified the search for new substrates or for the expansion of the use of substrates already in use, as well as the search for microorganisms with different metabolic capacities. In the present work, we isolated and tested a yeast from the soil of sugarcane irrigated with vinasse, that is, with high mineral content and acidic pH. The strain of Meyerozyma caribbica URM 8365 was able to ferment glucose, but the use of xylose occurred when some oxygenation was provided. However, some fermentation of xylose to ethanol in oxygen limitation also occurs if glucose was present. This strain was able to produce ethanol from molasses substrate with 76% efficiency, showing its tolerance to possible inhibitors. High ethanol production efficiencies were also observed in acidic hydrolysates of each bagasse, sorghum, and cactus pear biomass. Mixtures of these substrates were tested and the best composition was found for the use of excess plant biomass in supplementation of primary substrates. It was also possible to verify the production of xylitol from xylose when the acetic acid concentration is reduced. Finally, the proposed metabolic model allowed calculating how much of the xylose carbon can be directed to the production of ethanol and/or xylitol in the presence of glucose. With this, it is possible to design an industrial plant that combines the production of ethanol and/or xylitol using combinations of primary substrates with hydrolysates of their biomass.
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Affiliation(s)
- Bárbara Ribeiro Alves Alencar
- Laboratory of Biomass Energy, Department of Nuclear Energy, Federal University of Pernambuco, Recife 50670-901, Brazil; (B.R.A.A.); (S.P.d.S.); (E.D.D.)
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil; (R.A.A.d.F.); (R.K.S.); (C.E.)
| | - Renan Anderson Alves de Freitas
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil; (R.A.A.d.F.); (R.K.S.); (C.E.)
| | | | - Rayssa Karla Silva
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil; (R.A.A.d.F.); (R.K.S.); (C.E.)
- Laboratory of Microbial Metabolism, Institute of Biological Sciences, University of Pernambuco, Recife 50110-000, Brazil;
| | - Carolina Elsztein
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil; (R.A.A.d.F.); (R.K.S.); (C.E.)
| | - Suzyanne Porfírio da Silva
- Laboratory of Biomass Energy, Department of Nuclear Energy, Federal University of Pernambuco, Recife 50670-901, Brazil; (B.R.A.A.); (S.P.d.S.); (E.D.D.)
| | - Emmanuel Damilano Dutra
- Laboratory of Biomass Energy, Department of Nuclear Energy, Federal University of Pernambuco, Recife 50670-901, Brazil; (B.R.A.A.); (S.P.d.S.); (E.D.D.)
| | - Marcos Antonio de Morais Junior
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil; (R.A.A.d.F.); (R.K.S.); (C.E.)
| | - Rafael Barros de Souza
- Laboratory of Microbial Metabolism, Institute of Biological Sciences, University of Pernambuco, Recife 50110-000, Brazil;
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Identification of traits to improve co-assimilation of glucose and xylose by adaptive evolution of Spathaspora passalidarum and Scheffersomyces stipitis yeasts. Appl Microbiol Biotechnol 2023; 107:1143-1157. [PMID: 36625916 DOI: 10.1007/s00253-023-12362-1] [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: 08/26/2022] [Revised: 11/21/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
Abstract
Lignocellulosic biomass is a renewable raw material for producing several high-value-added chemicals and fuels. In general, xylose and glucose are the major sugars in biomass hydrolysates, and their efficient utilization by microorganisms is critical for an economical production process. Yeasts capable of co-consuming mixed sugars might lead to higher yields and productivities in industrial fermentation processes. Herein, we performed adaptive evolution assays with two xylose-fermenting yeasts, Spathaspora passalidarum and Scheffersomyces stipitis, to obtain derived clones with improved capabilities of glucose and xylose co-consumption. Adapted strains were obtained after successive growth selection using xylose and the non-metabolized glucose analog 2-deoxy-D-glucose as a selective pressure. The co-fermentation capacity of evolved and parental strains was evaluated on xylose-glucose mixtures. Our results revealed an improved co-assimilation capability by the evolved strains; however, xylose and glucose consumption were observed at slower rates than the parental yeasts. Genome resequencing of the evolved strains revealed genes affected by non-synonymous variants that might be involved with the co-consumption phenotype, including the HXT2.4 gene that encodes a putative glucose transporter in Sp. passalidarum. Expression of this mutant HXT2.4 in Saccharomyces cerevisiae improved the cells' co-assimilation of glucose and xylose. Therefore, our results demonstrated the successful improvement of co-fermentation through evolutionary engineering and the identification of potential targets for further genetic engineering of different yeast strains. KEY POINTS: • Laboratory evolution assay was used to obtain improved sugar co-consumption of non-Saccharomyces strains. • Evolved Sp. passalidarum and Sc. stipitis were able to more efficiently co-ferment glucose and xylose. • A mutant Hxt2.4 permease, which co-transports xylose and glucose, was identified.
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Fermentation performance of a Mexican native Clavispora lusitaniae strain for xylitol and ethanol production from xylose, glucose and cellobiose. Enzyme Microb Technol 2022; 160:110094. [PMID: 35810624 DOI: 10.1016/j.enzmictec.2022.110094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022]
Abstract
Lignocellulose hydrolysates are rich in fermentable sugars such as xylose, cellobiose and glucose, with high potential in the biotechnology industry to obtain bioproducts of higher economic value. Thus, it is important to search for and study new yeast strains that co-consume these sugars to achieve better yields and productivity in the processes. The yeast Clavispora lusitaniae CDBB-L-2031, a native strain isolated from mezcal must, was studied under various culture conditions to potentially produce ethanol and xylitol due to its ability to assimilate xylose, cellobiose and glucose. This yeast produced ethanol under microaerobic conditions with yields of 0.451 gethanol/gglucose and 0.344 gethanol/gcellobiose, when grown on 1% glucose or cellobiose, respectively. In mixtures (0.5% each) of glucose:xylose and glucose:xylose:cellobiose the yields were 0.367 gethanol/gGX and 0. 380 gethanol/gGXC, respectively. Likewise, in identical conditions, C. lusitaniae produced xylitol from xylose with a yield of 0.421 gxylitol/gxylose. In 5% glucose or xylose, this yeast had better ethanol and xylitol titers and yields, respectively. However, glucose negatively affected xylitol production in the mixture of both sugars (3% each), producing only ethanol. Xylose reductase (XR) and xylitol dehydrogenase (XDH) activities were evaluated in cultures growing on xylose or glucose, obtaining the highest values in cultures on xylose at 8 h (25.9 and 6.22 mU/mg, respectively). While in glucose cultures, XR and XDH activities were detected once this substrate was consumed (4.06 and 3.32 mU/mg, respectively). Finally, the XYL1 and XYL2 genes encoding xylose reductase and xylitol dehydrogenase, respectively, were up-regulated by xylose, whereas glucose down-regulated their expression.
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Heistinger L, Dohm JC, Paes BG, Koizar D, Troyer C, Ata Ö, Steininger-Mairinger T, Mattanovich D. Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization. Microb Cell Fact 2022; 21:70. [PMID: 35468837 PMCID: PMC9036795 DOI: 10.1186/s12934-022-01796-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The yeast genus Komagataella currently consists of seven methylotrophic species isolated from tree environments. Well-characterized strains of K. phaffii and K. pastoris are important hosts for biotechnological applications, but the potential of other species from the genus remains largely unexplored. In this study, we characterized 25 natural isolates from all seven described Komagataella species to identify interesting traits and provide a comprehensive overview of the genotypic and phenotypic diversity available within this genus. RESULTS Growth tests on different carbon sources and in the presence of stressors at two different temperatures allowed us to identify strains with differences in tolerance to high pH, high temperature, and growth on xylose. As Komagataella species are generally not considered xylose-utilizing yeasts, xylose assimilation was characterized in detail. Growth assays, enzyme activity measurements and 13C labeling confirmed the ability of K. phaffii to utilize D-xylose via the oxidoreductase pathway. In addition, we performed long-read whole-genome sequencing to generate genome assemblies of all Komagataella species type strains and additional K. phaffii and K. pastoris isolates for comparative analysis. All sequenced genomes have a similar size and share 83-99% average sequence identity. Genome structure analysis showed that K. pastoris and K. ulmi share the same rearrangements in difference to K. phaffii, while the genome structure of K. kurtzmanii is similar to K. phaffii. The genomes of the other, more distant species showed a larger number of structural differences. Moreover, we used the newly assembled genomes to identify putative orthologs of important xylose-related genes in the different Komagataella species. CONCLUSIONS By characterizing the phenotypes of 25 natural Komagataella isolates, we could identify strains with improved growth on different relevant carbon sources and stress conditions. Our data on the phenotypic and genotypic diversity will provide the basis for the use of so-far neglected Komagataella strains with interesting characteristics and the elucidation of the genetic determinants of improved growth and stress tolerance for targeted strain improvement.
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Affiliation(s)
- Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria.
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Barbara G Paes
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia (UnB), Brasilia, Brazil
| | - Daniel Koizar
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
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Physiological comparisons among Spathaspora passalidarum, Spathaspora arborariae, and Scheffersomyces stipitis reveal the bottlenecks for their use in the production of second-generation ethanol. Braz J Microbiol 2022; 53:977-990. [PMID: 35174461 PMCID: PMC9151973 DOI: 10.1007/s42770-022-00693-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/21/2021] [Indexed: 02/01/2023] Open
Abstract
The microbial conversion of pentoses to ethanol is one of the major drawbacks that limits the complete use of lignocellulosic sugars. In this study, we compared the yeast species Spathaspora arborariae, Spathaspora passalidarum, and Sheffersomyces stipitis regarding their potential use for xylose fermentation. Herein, we evaluated the effects of xylose concentration, presence of glucose, and temperature on ethanol production. The inhibitory effects of furfural, hydroxymethylfurfural (HMF), acetic acid, and ethanol were also determined. The highest ethanol yield (0.44 g/g) and productivity (1.02 g/L.h) were obtained using Sp. passalidarum grown in 100 g/L xylose at 32 °C. The rate of xylose consumption was reduced in the presence of glucose for the species tested. Hydroxymethylfurfural did not inhibit the growth of yeasts, whereas furfural extended their lag phase. Acetic acid inhibited the growth and fermentation of all yeasts. Furthermore, we showed that these xylose-fermenting yeasts do not produce ethanol concentrations greater than 4% (v/v), probably due to the inhibitory effects of ethanol on yeast physiology. Our data confirm that among the studied yeasts, Sp. passalidarum is the most promising for xylose fermentation, and the low tolerance to ethanol is an important aspect to be improved to increase its performance for second-generation (2G) ethanol production. Our molecular data showed that this yeast failed to induce the expression of some classical genes involved in ethanol tolerance. These findings suggest that Sp. passalidarum may have not activated a proper response to the stress, impacting its ability to overcome the negative effects of ethanol on the cells.
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MANJARRES-PINZÓN K, MENDOZA-MEZA D, ARIAS-ZABALA M, CORREA-LONDOÑO G, RODRIGUEZ-SANDOVAL E. Effects of agitation rate and dissolved oxygen on xylose reductase activity during xylitol production at bioreactor scale. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.04221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bae JH, Kim MJ, Sung BH, Jin YS, Sohn JH. Directed evolution and secretory expression of xylose isomerase for improved utilisation of xylose in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:223. [PMID: 34823570 PMCID: PMC8613937 DOI: 10.1186/s13068-021-02073-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Xylose contained in lignocellulosic biomass is an attractive carbon substrate for economically viable conversion to bioethanol. Extensive research has been conducted on xylose fermentation using recombinant Saccharomyces cerevisiae expressing xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways along with the introduction of a xylose transporter and amplification of the downstream pathway. However, the low utilization of xylose in the presence of glucose, due to the varying preference for cellular uptake, is a lingering challenge. Studies so far have mainly focused on xylose utilization inside the cells, but there have been little trials on the conversion of xylose to xylulose by cell before uptake. We hypothesized that the extracellular conversion of xylose to xylulose before uptake would facilitate better utilization of xylose even in the presence of glucose. To verify this, XI from Piromyces sp. was engineered and hyper-secreted in S. cerevisiae for the extracellular conversion of xylose to xylulose. RESULTS The optimal pH of XI was lowered from 7.0 to 5.0 by directed evolution to ensure its high activity under the acidic conditions used for yeast fermentation, and hyper-secretion of an engineered XI-76 mutant (E56A and I252M) was accomplished by employing target protein-specific translational fusion partners. The purified XI-76 showed twofold higher activity than that of the wild type at pH 5. The secretory expression of XI-76 in the previously developed xylose utilizing yeast strain, SR8 increased xylose consumption and ethanol production by approximately 7-20% and 15-20% in xylose fermentation and glucose and xylose co-fermentation, respectively. CONCLUSIONS Isomerisation of xylose to xylulose before uptake using extracellular XI was found to be effective in xylose fermentation or glucose/xylose co-fermentation. This suggested that glucose competed less with xylulose than with xylose for uptake by the cell. Consequently, the engineered XI secretion system constructed in this study can pave the way for simultaneous utilization of C5/C6 sugars from the sustainable lignocellulosic biomass.
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Affiliation(s)
- Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Mi-Jin Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- Cellapy Bio Inc., Bio-Venture Center 211, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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11
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Cellulosic Bioethanol from Industrial Eucalyptus globulus Bark Residues Using Kraft Pulping as a Pretreatment. ENERGIES 2021. [DOI: 10.3390/en14082185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The pulp and paper industry faces an emerging challenge for valorising wastes and side-streams generated according to the biorefinery concept. Eucalyptus globulus bark, an abundant industrial residue in the Portuguese pulp and paper sector, has a high potential to be converted into biobased products instead of being burned. This work aimed to evaluate the ethanol production from E. globulus bark previously submitted to kraft pulping through separate hydrolysis and fermentation (SHF) configuration. Fed-batch enzymatic hydrolysis provided a concentrated hydrolysate with 161.6 g·L−1 of cellulosic sugars. S. cerevisiae and Ethanol Red® strains demonstrated a very good fermentation performance, despite a negligible xylose consumption. S. passalidarum, a yeast known for its capability to consume pentoses, was studied in a simultaneous co-culture with Ethanol Red®. However, bioethanol production was not improved. The best fermentation performance was achieved by Ethanol Red®, which provided a maximum ethanol concentration near 50 g·L−1 and fermentation efficiency of 80%. Concluding, kraft pulp from E. globulus bark showed a high potential to be converted into cellulosic bioethanol, being susceptible to implementing an integrated biorefinery on the pulp and paper industrial plants.
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12
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Variable and dose-dependent response of Saccharomyces and non-Saccharomyces yeasts toward lignocellulosic hydrolysate inhibitors. Braz J Microbiol 2021; 52:575-586. [PMID: 33825150 DOI: 10.1007/s42770-021-00489-0] [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: 10/24/2020] [Accepted: 03/29/2021] [Indexed: 10/21/2022] Open
Abstract
Lignocellulosic hydrolysates will also contain compounds that inhibit microbial metabolism, such as organic acids, furaldehydes, and phenolic compounds. Understanding the response of yeasts toward such inhibitors is important to the development of different bioprocesses. In this work, the growth capacity of 7 industrial Saccharomyces cerevisiae and 7 non-Saccharomyces yeasts was compared in the presence of 3 different concentrations of furaldehydes (furfural and 5-hydroxymetil-furfural), organic acids (acetic and formic acids), and phenolic compounds (vanillin, syringaldehyde, ferulic, and coumaric acids). Then, Candida tropicalis JA2, Meyerozyma caribbica JA9, Wickerhamomyces anomalus 740, S. cerevisiae JP1, B1.1, and G06 were selected for fermentation in presence of acetic acid, HMF, and vanillin because they proved to be most tolerant to the tested compounds, while Spathaspora sp. JA1 because its xylose consumption rate. The results obtained showed a dose-dependent response of the yeasts toward the eight different inhibitors. Among the compared yeasts, S. cerevisiae strains presented higher tolerance than non-Saccharomyces, 3 of them with the highest tolerance among all. Regarding the non-Saccharomyces yeasts, C. tropicalis JA2 and W. anomalus 740 appeared as the most tolerant, whereas Spathaspora strains appeared very sensitive to the different compounds.
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13
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Enhanced Tolerance of Spathaspora passalidarum to Sugarcane Bagasse Hydrolysate for Ethanol Production from Xylose. Appl Biochem Biotechnol 2021; 193:2182-2197. [PMID: 33682050 DOI: 10.1007/s12010-021-03544-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
During the pretreatment and hydrolysis of lignocellulosic biomass to obtain a hydrolysate rich in fermentable sugars, furaldehydes (furfural and hydroxymethylfurfural), phenolic compounds, and organic acids are formed and released. These compounds inhibit yeast metabolism, reducing fermentation yields and productivity. This study initially confirmed the ability of Spathaspora passalidarum to ferment xylose and demonstrated its sensibility to the inhibitors present in the hemicellulosic sugarcane bagasse hydrolysate. Then, an adaptive laboratory evolution, with progressive increments of hydrolysate concentration, was employed to select a strain more resistant to hydrolysate inhibitors. Afterward, a central composite design was performed to maximize ethanol production using hydrolysate as substrate. At optimized conditions (initial cell concentration of 30 g/L), S. passalidarum was able to produce 19.4 g/L of ethanol with productivity, yield, and xylose consumption rate of 0.8 g/L.h and 0.4 g/g, respectively, in a sugarcane bagasse hemicellulosic hydrolysate. A kinetic model was developed to describe the inhibition of fermentation by substrate and product. The values obtained for substrate saturation and inhibition constant were Ks = 120.4 g/L and Ki = 1293.4 g/L. Ethanol concentration that stops cell growth was 30.1 g/L. There was an agreement between simulated and experimental results, with a residual standard deviation lower than 6%.
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14
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Abstract
In order to exploit a fast-growing Paulownia hardwood as an energy crop, a xylose-enriched hydrolysate was obtained in this work to increase the ethanol concentration using the hemicellulosic fraction, besides the already widely studied cellulosic fraction. For that, Paulownia elongata x fortunei was submitted to autohydrolysis treatment (210 °C or S0 of 4.08) for the xylan solubilization, mainly as xylooligosaccharides. Afterwards, sequential stages of acid hydrolysis, concentration, and detoxification were evaluated to obtain fermentable sugars. Thus, detoxified and non-detoxified hydrolysates (diluted or not) were fermented for ethanol production using a natural xylose-consuming yeast, Scheffersomyces stipitis CECT 1922, and an industrial Saccharomyces cerevisiae MEC1133 strain, metabolic engineered strain with the xylose reductase/xylitol dehydrogenase pathway. Results from fermentation assays showed that the engineered S. cerevisiae strain produced up to 14.2 g/L of ethanol (corresponding to 0.33 g/g of ethanol yield) using the non-detoxified hydrolysate. Nevertheless, the yeast S. stipitis reached similar values of ethanol, but only in the detoxified hydrolysate. Hence, the fermentation data prove the suitability and robustness of the engineered strain to ferment non-detoxified liquor, and the appropriateness of detoxification of liquor for the use of less robust yeast. In addition, the success of hemicellulose-to-ethanol production obtained in this work shows the Paulownia biomass as a suitable renewable source for ethanol production following a suitable fractionation process within a biorefinery approach.
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15
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Paes BG, Steindorff AS, Formighieri EF, Pereira IS, Almeida JRM. Physiological characterization and transcriptome analysis of Pichia pastoris reveals its response to lignocellulose-derived inhibitors. AMB Express 2021; 11:2. [PMID: 33389238 PMCID: PMC7779389 DOI: 10.1186/s13568-020-01170-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Abstract
The negative effects of lignocellulose-derived inhibitors such as acetic acid and furaldehydes on microbial metabolism constitute a significant drawback to the usage of biomass feedstocks for the production of fuels and chemicals. The yeast Pichia pastoris has shown a great biotechnological potential for producing heterologous proteins and renewable chemicals. Despite its relevance, the performance of P. pastoris in presence of lignocellulose-derived inhibitors remains unclear. In this work, our results show for the first time the dose-dependent response of P. pastoris to acetic acid, furaldehydes (HMF and furfural), and sugarcane biomass hydrolysate, both at physiological and transcriptional levels. The yeast was able to grow in synthetic media with up to 6 g.L-1 acetic acid, 1.75 g.L-1 furaldehydes or hydrolysate diluted to 10% (v/v). However, its metabolism was completely hindered in presence of hydrolysate diluted to 30% (v/v). Additionally, the yeast was capable to co-consume acetic acid and glucose. At the transcriptional level, P. pastoris response to lignocellulose-derived inhibitors relays on the up-regulation of genes related to transmembrane transport, oxidoreductase activities, RNA processing, and the repression of pathways related to biosynthetic processes and central carbon metabolism. These results demonstrate a polygenetic response that involves detoxification activities, and maintenance of energy and cellular homeostasis. In this context, ALD4, OYE3, QOR2, NTL100, YCT1, and PPR1 were identified as target genes to improve P. pastoris tolerance. Altogether, this work provides valuable insights into the P. pastoris stress tolerance, which can be useful to expand its use in different bioprocesses.
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Affiliation(s)
- Barbara G Paes
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
- Graduate Program of Molecular Biology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil
| | - Andrei Stecca Steindorff
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
| | - Eduardo F Formighieri
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
| | - Ildinete Silva Pereira
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
- Graduate Program of Molecular Biology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil
| | - João Ricardo M Almeida
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil.
- Graduate Program of Microbial Biology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil.
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16
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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17
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Atzmüller D, Ullmann N, Zwirzitz A. Identification of genes involved in xylose metabolism of Meyerozyma guilliermondii and their genetic engineering for increased xylitol production. AMB Express 2020; 10:78. [PMID: 32314068 PMCID: PMC7171046 DOI: 10.1186/s13568-020-01012-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
Meyerozyma guilliermondii, a non-conventional yeast that naturally assimilates xylose, is considered as a candidate for biotechnological production of the sugar alternative xylitol. Because the genes of the xylose metabolism were yet unknown, all efforts published so far to increase the xylitol yield of this yeast are limited to fermentation optimization. Hence, this study aimed to genetically engineer this organism for the first time with the objective to increase xylitol production. Therefore, the previously uncharacterized genes of M. guilliermondii ATCC 6260 encoding for xylose reductase (XR) and xylitol dehydrogenase (XDH) were identified by pathway investigations and sequence similarity analysis. Cloning and overexpression of the putative XR as well as knockout of the putative XDH genes generated strains with about threefold increased xylitol yield. Strains that combined both genetic modifications displayed fivefold increase in overall xylitol yield. Enzymatic activity assays with lysates of XR overexpressing and XDH knockout strains underlined the presumed functions of the respective genes. Furthermore, growth evaluation of the engineered strains on xylose as sole carbon source provides insights into xylose metabolism and its utilization for cell growth.![]()
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18
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Redox potential as a key parameter for monitoring and optimization of xylose fermentation with yeast Spathaspora passalidarum under limited-oxygen conditions. Bioprocess Biosyst Eng 2020; 43:1509-1519. [DOI: 10.1007/s00449-020-02344-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/02/2020] [Indexed: 01/04/2023]
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19
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The Xylose Metabolizing Yeast Spathaspora passalidarum is a Promising Genetic Treasure for Improving Bioethanol Production. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6010033] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Currently, the fermentation technology for recycling agriculture waste for generation of alternative renewable biofuels is getting more and more attention because of the environmental merits of biofuels for decreasing the rapid rise of greenhouse gas effects compared to petrochemical, keeping in mind the increase of petrol cost and the exhaustion of limited petroleum resources. One of widely used biofuels is bioethanol, and the use of yeasts for commercial fermentation of cellulosic and hemicellulosic agricultural biomasses is one of the growing biotechnological trends for bioethanol production. Effective fermentation and assimilation of xylose, the major pentose sugar element of plant cell walls and the second most abundant carbohydrate, is a bottleneck step towards a robust biofuel production from agricultural waste materials. Hence, several attempts were implemented to engineer the conventional Saccharomyces cerevisiae yeast to transport and ferment xylose because naturally it does not use xylose, using genetic materials of Pichia stipitis, the pioneer native xylose fermenting yeast. Recently, the nonconventional yeast Spathaspora passalidarum appeared as a founder member of a new small group of yeasts that, like Pichia stipitis, can utilize and ferment xylose. Therefore, the understanding of the molecular mechanisms regulating the xylose assimilation in such pentose fermenting yeasts will enable us to eliminate the obstacles in the biofuels pipeline, and to develop industrial strains by means of genetic engineering to increase the availability of renewable biofuel products from agricultural biomass. In this review, we will highlight the recent advances in the field of native xylose metabolizing yeasts, with special emphasis on S. passalidarum for improving bioethanol production.
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Xylitol Production: Identification and Comparison of New Producing Yeasts. Microorganisms 2019; 7:microorganisms7110484. [PMID: 31652879 PMCID: PMC6920771 DOI: 10.3390/microorganisms7110484] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 01/31/2023] Open
Abstract
Xylitol is a sugar alcohol with five carbons that can be used in the pharmaceutical and food industries. It is industrially produced by chemical route; however, a more economical and environmentally friendly production process is of interest. In this context, this study aimed to select wild yeasts able to produce xylitol and compare their performance in sugarcane bagasse hydrolysate. For this, 960 yeast strains, isolated from soil, wood, and insects have been prospected and selected for the ability to grow on defined medium containing xylose as the sole carbon source. A total of 42 yeasts was selected and their profile of sugar consumption and metabolite production were analyzed in microscale fermentation. The six best xylose-consuming strains were molecularly identified as Meyerozyma spp. The fermentative kinetics comparisons on defined medium and on sugarcane bagasse hydrolysate showed physiological differences among these strains. Production yields vary from YP/S = 0.25 g/g to YP/S = 0.34 g/g in defined medium and from YP/S = 0.41 g/g to YP/S = 0.60 g/g in the hydrolysate. Then, the xylitol production performance of the best xylose-consuming strain obtained in the screening, which was named M. guilliermondii B12, was compared with the previously reported xylitol producing yeasts M. guilliermondii A3, Spathaspora sp. JA1, and Wickerhamomyces anomalus 740 in sugarcane bagasse hydrolysate under oxygen-limited conditions. All the yeasts were able to metabolize xylose, but W. anomalus 740 showed the highest xylitol production yield, reaching a maximum of 0.83 g xylitol/g of xylose in hydrolysate. The screening strategy allowed identification of a new M. guilliermondii strain that efficiently grows in xylose even in hydrolysate with a high content of acetic acid (~6 g/L). In addition, this study reports, for the first time, a high-efficient xylitol producing strain of W. anomalus, which achieved, to the best of our knowledge, one of the highest xylitol production yields in hydrolysate reported in the literature.
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21
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Veras HCT, Campos CG, Nascimento IF, Abdelnur PV, Almeida JRM, Parachin NS. Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts. BMC Biotechnol 2019; 19:58. [PMID: 31382948 PMCID: PMC6683545 DOI: 10.1186/s12896-019-0548-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/19/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Efficient xylose fermentation still demands knowledge regarding xylose catabolism. In this study, metabolic flux analysis (MFA) and metabolomics were used to improve our understanding of xylose metabolism. Thus, a stoichiometric model was constructed to simulate the intracellular carbon flux and used to validate the metabolome data collected within xylose catabolic pathways of non-Saccharomyces xylose utilizing yeasts. RESULTS A metabolic flux model was constructed using xylose fermentation data from yeasts Scheffersomyces stipitis, Spathaspora arborariae, and Spathaspora passalidarum. In total, 39 intracellular metabolic reactions rates were utilized validating the measurements of 11 intracellular metabolites, acquired by mass spectrometry. Among them, 80% of total metabolites were confirmed with a correlation above 90% when compared to the stoichiometric model. Among the intracellular metabolites, fructose-6-phosphate, glucose-6-phosphate, ribulose-5-phosphate, and malate are validated in the three studied yeasts. However, the metabolites phosphoenolpyruvate and pyruvate could not be confirmed in any yeast. Finally, the three yeasts had the metabolic fluxes from xylose to ethanol compared. Xylose catabolism occurs at twice-higher flux rates in S. stipitis than S. passalidarum and S. arborariae. Besides, S. passalidarum present 1.5 times high flux rate in the xylose reductase reaction NADH-dependent than other two yeasts. CONCLUSIONS This study demonstrated a novel strategy for metabolome data validation and brought insights about naturally xylose-fermenting yeasts. S. stipitis and S. passalidarum showed respectively three and twice higher flux rates of XR with NADH cofactor, reducing the xylitol production when compared to S. arborariae. Besides then, the higher flux rates directed to pentose phosphate pathway (PPP) and glycolysis pathways resulted in better ethanol production in S. stipitis and S. passalidarum when compared to S. arborariae.
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Affiliation(s)
- Henrique C. T. Veras
- Grupo Engenharia de Biocatalisadores, Universidade de Brasília - UnB , Campus Darcy Ribeiro, Instituto de Ciências Biológicas, Bloco K, 1° andar, Asa Norte, Brasilia, 70.790-900 Brazil
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
| | - Christiane G. Campos
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
- Instituto de Química, Universidade Federal de Goiás - UFG, Goiânia, Brazil
| | - Igor F. Nascimento
- Programa de Pós-Graduação em Administração, Universidade de Brasília - UnB, Brasília, Brazil
| | - Patrícia V. Abdelnur
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
- Instituto de Química, Universidade Federal de Goiás - UFG, Goiânia, Brazil
| | - João R. M. Almeida
- Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA Agroenergia, Brasília-DF, Brazil
- Programa de Pós-Graduação em Biologia Microbiana, Instituto de Biologia, Universidade de Brasília - UnB, Brasilia, Brazil
| | - Nádia S. Parachin
- Grupo Engenharia de Biocatalisadores, Universidade de Brasília - UnB , Campus Darcy Ribeiro, Instituto de Ciências Biológicas, Bloco K, 1° andar, Asa Norte, Brasilia, 70.790-900 Brazil
- Programa de Pós-Graduação em Biologia Microbiana, Instituto de Biologia, Universidade de Brasília - UnB, Brasilia, Brazil
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Borelli G, Fiamenghi MB, dos Santos LV, Carazzolle MF, Pereira GAG, José J. Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts' Fermentation in Industry. Genome Biol Evol 2019; 11:1923-1938. [PMID: 31070742 PMCID: PMC6637916 DOI: 10.1093/gbe/evz036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Xylose assimilation and fermentation are important traits for second generation ethanol production. However, some genomic features associated with this pentose sugar's metabolism remain unknown in yeasts. Comparative genomics studies have led to important insights in this field, but we are still far from completely understanding endogenous yeasts' xylose metabolism. In this work, we carried out a deep evolutionary analysis suited for comparative genomics of xylose-consuming yeasts, searching for of positive selection on genes associated with glucose and xylose metabolism in the xylose-fermenters' clade. Our investigation detected positive selection fingerprints at this clade not only among sequences of important genes for xylose metabolism, such as xylose reductase and xylitol dehydrogenase, but also in genes expected to undergo neutral evolution, such as the glycolytic gene phosphoglycerate mutase. In addition, we present expansion, positive selection marks, and convergence as evidence supporting the hypothesis that natural selection is shaping the evolution of the little studied methylglyoxal reductases. We propose a metabolic model suggesting that selected codons among these proteins caused a putative change in cofactor preference from NADPH to NADH that alleviates cellular redox imbalance. These findings provide a wider look into pentose metabolism of yeasts and add this previously overlooked piece into the intricate puzzle of oxidative imbalance. Although being extensively discussed in evolutionary works the awareness of selection patterns is recent in biotechnology researches, rendering insights to surpass the reached status quo in many of its subareas.
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Affiliation(s)
- Guilherme Borelli
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Mateus Bernabe Fiamenghi
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Juliana José
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
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23
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Trichez D, Steindorff AS, Soares CEVF, Formighieri EF, Almeida JRM. Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production. FEMS Yeast Res 2019; 19:5480466. [DOI: 10.1093/femsyr/foz034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/25/2019] [Indexed: 12/30/2022] Open
Abstract
ABSTRACT
Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far.
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Affiliation(s)
- Débora Trichez
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
| | - Andrei S Steindorff
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
| | - Carlos E V F Soares
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
- Graduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Brasília, Campus Darcy Ribeiro, Postal code 70.910-900, Brasília-DF, Brazil
| | - Eduardo F Formighieri
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
| | - João R M Almeida
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
- Graduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Brasília, Campus Darcy Ribeiro, Postal code 70.910-900, Brasília-DF, Brazil
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24
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Shin M, Kim JW, Ye S, Kim S, Jeong D, Lee DY, Kim JN, Jin YS, Kim KH, Kim SR. Comparative global metabolite profiling of xylose-fermenting Saccharomyces cerevisiae SR8 and Scheffersomyces stipitis. Appl Microbiol Biotechnol 2019; 103:5435-5446. [PMID: 31001747 DOI: 10.1007/s00253-019-09829-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/18/2019] [Accepted: 04/04/2019] [Indexed: 01/22/2023]
Abstract
Bioconversion of lignocellulosic biomass into ethanol requires efficient xylose fermentation. Previously, we developed an engineered Saccharomyces cerevisiae strain, named SR8, through rational and inverse metabolic engineering strategies, thereby improving its xylose fermentation and ethanol production. However, its fermentation characteristics have not yet been fully evaluated. In this study, we investigated the xylose fermentation and metabolic profiles for ethanol production in the SR8 strain compared with native Scheffersomyces stipitis. The SR8 strain showed a higher maximum ethanol titer and xylose consumption rate when cultured with a high concentration of xylose, mixed sugars, and under anaerobic conditions than Sch. stipitis. However, its ethanol productivity was less on 40 g/L xylose as the sole carbon source, mainly due to the formation of xylitol and glycerol. Global metabolite profiling indicated different intracellular production rates of xylulose and glycerol-3-phosphate in the two strains. In addition, compared with Sch. stipitis, SR8 had increased abundances of metabolites from sugar metabolism and decreased abundances of metabolites from energy metabolism and free fatty acids. These results provide insights into how to control and balance redox cofactors for the production of fuels and chemicals from xylose by the engineered S. cerevisiae.
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Affiliation(s)
- Minhye Shin
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Jeong-Won Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Sooah Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Do Yup Lee
- Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, Korea
| | - Jong Nam Kim
- Department of Food Science and Nutrition, Dongseo University, Busan, Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, the University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea.
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25
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Collograi KC, da Costa AC, Ienczak JL. Effect of contamination with Lactobacillus fermentum I2 on ethanol production by Spathaspora passalidarum. Appl Microbiol Biotechnol 2019; 103:5039-5050. [DOI: 10.1007/s00253-019-09779-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/06/2019] [Accepted: 03/15/2019] [Indexed: 12/23/2022]
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26
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The production of ethanol from lignocellulosic biomass by Kluyveromyces marxianus CICC 1727-5 and Spathaspora passalidarum ATCC MYA-4345. Appl Microbiol Biotechnol 2019; 103:2845-2855. [DOI: 10.1007/s00253-019-09625-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/18/2018] [Accepted: 12/16/2018] [Indexed: 11/25/2022]
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27
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Guo Z, Wang Y, Hou Q, Li W, Zhao H, Sun Z, Zhang Z. Halobasidium xiangyangense gen. nov., sp. nov., a new xylose-utilizing yeast in the family Cystobasidiaceae, isolated from the pickling sauce used to make Datoucai, a high-salt fermented food. Int J Syst Evol Microbiol 2019; 69:139-145. [PMID: 30614783 DOI: 10.1099/ijsem.0.003119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we describe a new genus and species of yeast with high-salt tolerance. The strain was isolated from the pickling sauce used to make Datoucai, a traditional fermented food made from Brassica juncea in Xiangyang, China. Phylogenetic analysis of sequences from the D1/D2 region of the LSU rRNA gene and from the ITS region demonstrated that the strain, reference HBUAS51001T, was most closely related to members of the genera Occultifur and Cystobasidium. However, the greatest similarities between the D1/D2 and ITS nucleotide sequences of strain HBUAS51001T and the most closely related type strains from Occultifur and Cystobasidium were only 91 and 92 %, respectively. This suggests that strain HBUAS51001T does not belong to any currently described species. Strain HBUAS51001T grew readily on media in which xylose was the sole carbon source. The major ubiquinone was Q9. The genome of strain HBUAS51001T was 42.42 Mb with a G+C content of 53.93 mol%. Three candidate genes associated with xylose metabolism were identified. On the basis of genotypic and phenotypic data, strain HBUAS51001T can be considered as both a new species and a new genus, for which the name Halobasidium xiangyangense gen. nov., sp. nov. is proposed. The type strain is HBUAS51001T (=KCTC27810T=GDMCC 2.231T=CCTCC AY 2018002T).
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Affiliation(s)
- Zhuang Guo
- 1Northwest Hubei Research Institute of Traditional Fermented Food, College of Food Science and Technology, Hubei University of Arts and Science, Xiangyang, Hubei, PR China
| | - Yurong Wang
- 1Northwest Hubei Research Institute of Traditional Fermented Food, College of Food Science and Technology, Hubei University of Arts and Science, Xiangyang, Hubei, PR China
| | - Qiangchuan Hou
- 2Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Weicheng Li
- 2Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Huijun Zhao
- 1Northwest Hubei Research Institute of Traditional Fermented Food, College of Food Science and Technology, Hubei University of Arts and Science, Xiangyang, Hubei, PR China
| | - Zhihong Sun
- 2Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Zhendong Zhang
- 1Northwest Hubei Research Institute of Traditional Fermented Food, College of Food Science and Technology, Hubei University of Arts and Science, Xiangyang, Hubei, PR China
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