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Riedl A, Bojková D, Tan J, Jeney Á, Larsen PK, Jeney C, Full F, Kalinke U, Ruzsics Z. Construction and Characterization of a High-Capacity Replication-Competent Murine Cytomegalovirus Vector for Gene Delivery. Vaccines (Basel) 2024; 12:791. [PMID: 39066429 PMCID: PMC11281640 DOI: 10.3390/vaccines12070791] [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: 06/13/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
We investigated the basic characteristics of a new murine cytomegalovirus (MCMV) vector platform. Using BAC technology, we engineered replication-competent recombinant MCMVs with deletions of up to 26% of the wild-type genome. To this end, we targeted five gene blocks (m01-m17, m106-m109, m129-m141, m144-m158, and m159-m170). BACs featuring deletions from 18% to 26% of the wild-type genome exhibited delayed virus reconstitution, while smaller deletions (up to 16%) demonstrated reconstitution kinetics similar to those of the wild type. Utilizing an innovative methodology, we introduced large genomic DNA segments, up to 35 kbp, along with reporter genes into a newly designed vector with a potential cloning capacity of 46 kbp (Q4). Surprisingly, the insertion of diverse foreign DNAs alleviated the delayed plaque formation phenotype of Q4, and these large inserts remained stable through serial in vitro passages. With reporter-gene-expressing recombinant MCMVs, we successfully transduced not only mouse cell lines but also non-rodent mammalian cells, including those of human, monkey, bovine, and bat origin. Remarkably, even non-mammalian cell lines derived from chickens exhibited successful transduction.
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Affiliation(s)
- André Riedl
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany (F.F.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Denisa Bojková
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany (F.F.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Institute of Medical Virology, Goethe University Frankfurt, University Hospital, 60596 Frankfurt am Main, Germany
| | - Jiang Tan
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany (F.F.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Ábris Jeney
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Pia-Katharina Larsen
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hanover Medical School and the Helmholtz Centre for Infection Research, Institute for Experimental Infection Research, 30625 Hanover, Germany
| | - Csaba Jeney
- Department of Microsystems Engineering—IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Florian Full
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany (F.F.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Ulrich Kalinke
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hanover Medical School and the Helmholtz Centre for Infection Research, Institute for Experimental Infection Research, 30625 Hanover, Germany
| | - Zsolt Ruzsics
- Medical Center, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany (F.F.)
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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2
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Ying ZH, Mao CL, Xie W, Yu CH. Postbiotics in rheumatoid arthritis: emerging mechanisms and intervention perspectives. Front Microbiol 2023; 14:1290015. [PMID: 38029106 PMCID: PMC10662086 DOI: 10.3389/fmicb.2023.1290015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Rheumatoid arthritis (RA) is a prevalent chronic autoimmune disease that affects individuals of all age groups. Recently, the association between RA and the gut microbiome has led to the investigation of postbiotics as potential therapeutic strategies. Postbiotics refer to inactivated microbial cells, cellular components, or their metabolites that are specifically intended for the microbiota. Postbiotics not only profoundly influence the occurrence and development of RA, but they also mediate various inflammatory pathways, immune processes, and bone metabolism. Although they offer a variety of mechanisms and may even be superior to more conventional "biotics" such as probiotics and prebiotics, research on their efficacy and clinical significance in RA with disruptions to the intestinal microbiota remains limited. In this review, we provide an overview of the concept of postbiotics and summarize the current knowledge regarding postbiotics and their potential use in RA therapy. Postbiotics show potential as a viable adjunctive therapy option for RA.
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Affiliation(s)
- Zhen-Hua Ying
- Zhejiang Key Laboratory of Arthritis Diagnosis and Research, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Cheng-Liang Mao
- Zhejiang Key Laboratory of Arthritis Diagnosis and Research, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Zhejiang University of Technology, Hangzhou, China
| | - Wei Xie
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, China
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Chen-Huan Yu
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, China
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
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3
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Muller G, de Godoy VR, Dário MG, Duval EH, Alves-Jr SL, Bücker A, Rosa CA, Dunn B, Sherlock G, Stambuk BU. Improved Sugarcane-Based Fermentation Processes by an Industrial Fuel-Ethanol Yeast Strain. J Fungi (Basel) 2023; 9:803. [PMID: 37623574 PMCID: PMC10456111 DOI: 10.3390/jof9080803] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
In Brazil, sucrose-rich broths (cane juice and/or molasses) are used to produce billions of liters of both fuel ethanol and cachaça per year using selected Saccharomyces cerevisiae industrial strains. Considering the important role of feedstock (sugar) prices in the overall process economics, to improve sucrose fermentation the genetic characteristics of a group of eight fuel-ethanol and five cachaça industrial yeasts that tend to dominate the fermentors during the production season were determined by array comparative genomic hybridization. The widespread presence of genes encoding invertase at multiple telomeres has been shown to be a common feature of both baker's and distillers' yeast strains, and is postulated to be an adaptation to sucrose-rich broths. Our results show that only two strains (one fuel-ethanol and one cachaça yeast) have amplification of genes encoding invertase, with high specific activity. The other industrial yeast strains had a single locus (SUC2) in their genome, with different patterns of invertase activity. These results indicate that invertase activity probably does not limit sucrose fermentation during fuel-ethanol and cachaça production by these industrial strains. Using this knowledge, we changed the mode of sucrose metabolism of an industrial strain by avoiding extracellular invertase activity, overexpressing the intracellular invertase, and increasing its transport through the AGT1 permease. This approach allowed the direct consumption of the disaccharide by the cells, without releasing glucose or fructose into the medium, and a 11% higher ethanol production from sucrose by the modified industrial yeast, when compared to its parental strain.
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Affiliation(s)
- Gabriela Muller
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Victor R. de Godoy
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Marcelo G. Dário
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Eduarda H. Duval
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Sergio L. Alves-Jr
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Augusto Bücker
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Carlos A. Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil;
| | - Barbara Dunn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; (B.D.); (G.S.)
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; (B.D.); (G.S.)
| | - Boris U. Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
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4
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Eliodório KP, Cunha GCDGE, Lino FSDO, Sommer MOA, Gombert AK, Giudici R, Basso TO. Physiology of Saccharomyces cerevisiae during growth on industrial sugar cane molasses can be reproduced in a tailor-made defined synthetic medium. Sci Rep 2023; 13:10567. [PMID: 37386049 PMCID: PMC10310838 DOI: 10.1038/s41598-023-37618-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023] Open
Abstract
Fully defined laboratory media have the advantage of allowing for reproducibility and comparability of results among different laboratories, as well as being suitable for the investigation of how different individual components affect microbial or process performance. We developed a fully defined medium that mimics sugarcane molasses, a frequently used medium in different industrial processes where yeast is cultivated. The medium, named 2SMol, builds upon a previously published semi-defined formulation and is conveniently prepared from some stock solutions: C-source, organic N, inorganic N, organic acids, trace elements, vitamins, Mg + K, and Ca. We validated the 2SMol recipe in a scaled-down sugarcane biorefinery model, comparing the physiology of Saccharomyces cerevisiae in different actual molasses-based media. We demonstrate the flexibility of the medium by investigating the effect of nitrogen availability on the ethanol yield during fermentation. Here we present in detail the development of a fully defined synthetic molasses medium and the physiology of yeast strains in this medium compared to industrial molasses. This tailor-made medium was able to satisfactorily reproduce the physiology of S. cerevisiae in industrial molasses. Thus, we hope the 2SMol formulation will be valuable to researchers both in academia and industry to obtain new insights and developments in industrial yeast biotechnology.
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Affiliation(s)
- Kevy Pontes Eliodório
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo, Av. Prof. Luciano Gualberto, 380, São Paulo, SP, 05508-010, Brazil
| | - Gabriel Caetano de Gois E Cunha
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo, Av. Prof. Luciano Gualberto, 380, São Paulo, SP, 05508-010, Brazil
| | | | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Andreas Karoly Gombert
- School of Food Engineering, University of Campinas, R. Monteiro Lobato 80, Campinas, 13083-862, Brazil
| | - Reinaldo Giudici
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo, Av. Prof. Luciano Gualberto, 380, São Paulo, SP, 05508-010, Brazil
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo, Av. Prof. Luciano Gualberto, 380, São Paulo, SP, 05508-010, Brazil.
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Wu Y, Li B, Miao B, Xie C, Tang YQ. Saccharomyces cerevisiae employs complex regulation strategies to tolerate low pH stress during ethanol production. Microb Cell Fact 2022; 21:247. [DOI: 10.1186/s12934-022-01974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Industrial bioethanol production may involve a low pH environment caused by inorganic acids, improving the tolerance of Saccharomyces cerevisiae to a low pH environment is of industrial importance to increase ethanol yield, control bacterial contamination, and reduce production cost. In our previous study, acid tolerance of a diploid industrial Saccharomyces cerevisiae strain KF-7 was chronically acclimatized by continuous ethanol fermentation under gradually increasing low-pH stress conditions. Two haploid strains B3 and C3 having excellent low pH tolerance were derived through the sporulation of an isolated mutant. Diploid strain BC3 was obtained by mating these two haploids. In this study, B3, C3, BC3, and the original strain KF-7 were subjected to comparison transcriptome analysis to investigate the molecular mechanism of the enhanced phenotype.
Result
The comparison transcriptome analysis results suggested that the upregulated vitamin B1 and B6 biosynthesis contributed to the low pH tolerance. Amino acid metabolism, DNA repairment, and general stress response might also alleviate low pH stress.
Conclusion
Saccharomyces cerevisiae seems to employ complex regulation strategies to tolerate low pH during ethanol production. The findings provide guides for the construction of low pH-tolerant industrial strains that can be used in industrial fermentation processes.
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Tadioto V, Deoti JR, Müller C, de Souza BR, Fogolari O, Purificação M, Giehl A, Deoti L, Lucaroni AC, Matsushika A, Treichel H, Stambuk BU, Alves Junior SL. Prospecting and engineering yeasts for ethanol production under inhibitory conditions: an experimental design analysis. Bioprocess Biosyst Eng 2022:10.1007/s00449-022-02812-x. [DOI: 10.1007/s00449-022-02812-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022]
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7
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Increasing Ethanol Tolerance and Ethanol Production in an Industrial Fuel Ethanol Saccharomyces cerevisiae Strain. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8100470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The stress imposed by ethanol to Saccharomyces cerevisiae cells are one of the most challenging limiting factors in industrial fuel ethanol production. Consequently, the toxicity and tolerance to high ethanol concentrations has been the subject of extensive research, allowing the identification of several genes important for increasing the tolerance to this stress factor. However, most studies were performed with well-characterized laboratory strains, and how the results obtained with these strains work in industrial strains remains unknown. In the present work, we have tested three different strategies known to increase ethanol tolerance by laboratory strains in an industrial fuel–ethanol producing strain: the overexpression of the TRP1 or MSN2 genes, or the overexpression of a truncated version of the MSN2 gene. Our results show that the industrial CAT-1 strain tolerates up to 14% ethanol, and indeed the three strategies increased its tolerance to ethanol. When these strains were subjected to fermentations with high sugar content and cell recycle, simulating the industrial conditions used in Brazilian distilleries, only the strain with overexpression of the truncated MSN2 gene showed improved fermentation performance, allowing the production of 16% ethanol from 33% of total reducing sugars present in sugarcane molasses. Our results highlight the importance of testing genetic modifications in industrial yeast strains under industrial conditions in order to improve the production of industrial fuel ethanol by S. cerevisiae.
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8
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Dainton AN, Miller MF, White B, Lambrakis L, Aldrich CG. Composition and thermal processing evaluation of yeast ingredients as thiamin sources compared to a standard vitamin premix for canned cat food. PLoS One 2022; 17:e0271600. [PMID: 35917321 PMCID: PMC9345363 DOI: 10.1371/journal.pone.0271600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/03/2022] [Indexed: 11/18/2022] Open
Abstract
Significant improvement in thiamin retention of canned cat food has not been achieved by altering processing conditions. Some ingredients, such as yeasts, may supply thiamin able to withstand thermal processing. Therefore, the study objective was to evaluate yeast ingredients as thiamin sources for canned cat food. Six yeast ingredients were screened for thiamin content, and values ranged from 9.9–4,283.8 mg/kg dry matter basis (DMB). Treatments for thermal processing were arranged as a 2×4 factorial with 2 levels of vitamin premix (with or without) and 4 yeast ingredients (NY = none and LBV, BY, or EA from the ingredient screening). Replicates (n = 3) were processed in a horizontal still retort to an average lethality of 79.23 minutes. Thiamin degradation was analyzed as a mixed model with pre-retort thiamin content as a covariate and production day as a random effect. Main effects of vitamin premix and yeast and their interaction were significant at P-values less than 0.05. The Fisher’s LSD post hoc comparison test was used to separate means. On average, experimental formulas retained 33.75% thiamin. The main effect of vitamin premix (average -42.9 mg/kg DMB) was not significant (P > 0.05). Thiamin degradation between NY (-31.3 mg/kg DMB) and BY (-33.8 mg/kg DMB) was similar (P > 0.05) whereas EA (-40.5 mg/kg DMB) and LBV (-55.6 mg/kg DMB) lost more (P < 0.05) thiamin than NY. The experimental formula of EA with vitamin premix (-70.3 mg/kg DMB) lost more (P < 0.05) thiamin than no yeast, BY, or EA without vitamin premix (average -17.4 mg/kg DMB) and all others (average -57.3 mg/kg DMB) were intermediate (P > 0.05). In summary, thiamin from yeast ingredients didn’t exhibit better thermal stability than thiamin mononitrate. However, those ingredients with similar degradation levels or uniquely high thiamin levels may provide added value.
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Affiliation(s)
- Amanda N. Dainton
- Department of Grain Science & Industry, Kansas State University, Manhattan, KS, United States of America
| | - Markus F. Miller
- Simmons Pet Food, Inc, Siloam Springs, AR, United States of America
| | - Brittany White
- Simmons Pet Food, Inc, Siloam Springs, AR, United States of America
| | - Leah Lambrakis
- Simmons Pet Food, Inc, Siloam Springs, AR, United States of America
| | - Charles Gregory Aldrich
- Department of Grain Science & Industry, Kansas State University, Manhattan, KS, United States of America
- * E-mail:
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9
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Genotypic and phenotypic characterization of industrial autochthonous Saccharomyces cerevisiae for the selection of well-adapted bioethanol-producing strains. Fungal Biol 2022; 126:658-673. [DOI: 10.1016/j.funbio.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
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10
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High Foam Phenotypic Diversity and Variability in Flocculant Gene Observed for Various Yeast Cell Surfaces Present as Industrial Contaminants. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7030127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many contaminant yeast strains that survive inside fuel ethanol industrial vats show detrimental cell surface phenotypes. These harmful effects may include filamentation, invasive growth, flocculation, biofilm formation, and excessive foam production. Previous studies have linked some of these phenotypes to the expression of FLO genes, and the presence of gene length polymorphisms causing the expansion of FLO gene size appears to result in stronger flocculation and biofilm formation phenotypes. We performed here a molecular analysis of FLO1 and FLO11 gene polymorphisms present in contaminant strains of Saccharomyces cerevisiae from Brazilian fuel ethanol distilleries showing vigorous foaming phenotypes during fermentation. The size variability of these genes was correlated with cellular hydrophobicity, flocculation, and highly foaming phenotypes in these yeast strains. Our results also showed that deleting the primary activator of FLO genes (the FLO8 gene) from the genome of a contaminant and highly foaming industrial strain avoids complex foam formation, flocculation, invasive growth, and biofilm production by the engineered (flo8∆::BleR/flo8Δ::kanMX) yeast strain. Thus, the characterization of highly foaming yeasts and the influence of FLO8 in this phenotype open new perspectives for yeast strain engineering and optimization in the sugarcane fuel-ethanol industry.
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11
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Saccharomyces cerevisiae strains used industrially for bioethanol production. Essays Biochem 2021; 65:147-161. [PMID: 34156078 DOI: 10.1042/ebc20200160] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 01/21/2023]
Abstract
Fuel ethanol is produced by the yeast Saccharomyces cerevisiae mainly from corn starch in the United States and from sugarcane sucrose in Brazil, which together manufacture ∼85% of a global yearly production of 109.8 million m3 (in 2019). While in North America genetically engineered (GE) strains account for ∼80% of the ethanol produced, including strains that express amylases and are engineered to produce higher ethanol yields; in South America, mostly (>90%) non-GE strains are used in ethanol production, primarily as starters in non-aseptic fermentation systems with cell recycling. In spite of intensive research exploring lignocellulosic ethanol (or second generation ethanol), this option still accounts for <1% of global ethanol production. In this mini-review, we describe the main aspects of fuel ethanol production, emphasizing bioprocesses operating in North America and Brazil. We list and describe the main properties of several commercial yeast products (i.e., yeast strains) that are available worldwide to bioethanol producers, including GE strains with their respective genetic modifications. We also discuss recent studies that have started to shed light on the genes and traits that are important for the persistence and dominance of yeast strains in the non-aseptic process in Brazil. While Brazilian bioethanol yeast strains originated from a historical process of domestication for sugarcane fermentation, leading to a unique group with significant economic applications, in U.S.A., guided selection, breeding and genetic engineering approaches have driven the generation of new yeast products for the market.
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Jacobus AP, Stephens TG, Youssef P, González-Pech R, Ciccotosto-Camp MM, Dougan KE, Chen Y, Basso LC, Frazzon J, Chan CX, Gross J. Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts. Front Microbiol 2021; 12:644089. [PMID: 33936002 PMCID: PMC8082247 DOI: 10.3389/fmicb.2021.644089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 01/05/2023] Open
Abstract
Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288C and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of a particular family of SAM-dependent methyl transferases, rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.
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Affiliation(s)
- Ana Paula Jacobus
- Laboratory for Genomics and Experimental Evolution of Yeasts, Institute for Bioenergy Research, São Paulo State University, Rio Claro, Brazil
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre Youssef
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Raul González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael M Ciccotosto-Camp
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine E Dougan
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Luiz Carlos Basso
- Biological Science Department, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo (USP), Piracicaba, Brazil
| | - Jeverson Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jeferson Gross
- Laboratory for Genomics and Experimental Evolution of Yeasts, Institute for Bioenergy Research, São Paulo State University, Rio Claro, Brazil
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Ceccato-Antonini SR, Covre EA. From baker's yeast to genetically modified budding yeasts: the scientific evolution of bioethanol industry from sugarcane. FEMS Yeast Res 2020; 20:6021367. [PMID: 33406233 DOI: 10.1093/femsyr/foaa065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/02/2020] [Indexed: 12/22/2022] Open
Abstract
The peculiarities of Brazilian fuel ethanol fermentation allow the entry of native yeasts that may dominate over the starter strains of Saccharomyces cerevisiae and persist throughout the sugarcane harvest. The switch from the use of baker's yeast as starter to selected budding yeasts obtained by a selective pressure strategy was followed by a wealth of genomic information that enabled the understanding of the superiority of selected yeast strains. This review describes how the process of yeast selection evolved in the sugarcane-based bioethanol industry, the selection criteria and recent advances in genomics that could advance the fermentation process. The prospective use of genetically modified yeast strains, specially designed for increased robustness and product yield, with special emphasis on those obtained by the CRISPR (clustered regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) genome-editing approach, is discussed as a possible solution to confer higher performance and stability to the fermentation process for fuel ethanol production.
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Affiliation(s)
- Sandra Regina Ceccato-Antonini
- Laboratory of Agricultural and Molecular Microbiology, Dept Tecnologia Agroindustrial e Socioeconomia Rural, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Via Anhanguera, km 174, 13600-970 Araras, São Paulo State, Brazil
| | - Elizabete Aparecida Covre
- Laboratory of Agricultural and Molecular Microbiology, Dept Tecnologia Agroindustrial e Socioeconomia Rural, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Via Anhanguera, km 174, 13600-970 Araras, São Paulo State, Brazil
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Vijayalakshmi S, Govindarajan M, Al-Mulahim N, Ahmed Z, Mahboob S. Cellulase immobilized magnetic nanoparticles for green energy production from Allamanda schottii L: Sustainability research in waste recycling. Saudi J Biol Sci 2020; 28:901-910. [PMID: 33424382 PMCID: PMC7783813 DOI: 10.1016/j.sjbs.2020.11.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 11/25/2022] Open
Abstract
This study presents ethanol's fabrication by fermenting the golden trumpet flower (Allamanda schottii L) with the yeast strain Saccharomyces cerevisiae. The changes in different parameters during fermentation were studied and optimized while producing the ethanol and the end product was subjected to emission test study by blending petrol and ethanol. The Allamanda floral substrate contains 65% polysaccharides. The strain S. cerevisiae was obtained in the form of baker's yeast from a domestic shop. For 100 ml of slurry, the highest bioethanol yield recorded was about 18.75 ml via optimization of different culture conditions, including a 1:8 ratio for slurry preparation, maintained under 35 ⁰C, 5.5 pH, 72 h. old inoculum with a quantity of 3.75 g 100 ml-1, fermented for120 h. The highest yield of bioethanol was acquired under the addition of urea. This technique & design is capable of industrial-scale fabrication of bioethanol by using A. schottii floral substrates. This research was conducted to fabricate ethanol by fermentation (A. schottii L) floral substrate with S. cerevisiae. The optimum physiochemical parameters required to obtain the highest yield of bioethanol from A. schottii flower by fermentation was studied. The immobilization strategy with a cheap agricultural substrate and magnetic nanoparticles were also studied. The engine performance and emission studies were done with different blends of petrol and bio-ethanol.
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Affiliation(s)
| | - Marimuthu Govindarajan
- Department of Zoology, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India.,Unit of Natural Products and Nanotechnology, Department of Zoology, Government College for Women (Autonomous), Kumbakonam 612 001, Tamil Nadu, India
| | - Norah Al-Mulahim
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Zubair Ahmed
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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15
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Becerra-Rodríguez C, Marsit S, Galeote V. Diversity of Oligopeptide Transport in Yeast and Its Impact on Adaptation to Winemaking Conditions. Front Genet 2020; 11:602. [PMID: 32587604 PMCID: PMC7298112 DOI: 10.3389/fgene.2020.00602] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Nitrogen is an essential nutrient for yeasts and its relative abundance is an important modulator of fermentation kinetics. The main sources of nitrogen in food are ammonium and free amino acids, however, secondary sources such as oligopeptides are also important contributors to the nitrogen supply. In yeast, oligopeptide uptake is driven by different families of proton–coupled transporters whose specificity depends on peptide length. Proton-dependent Oligopeptide Transporters (POT) are specific to di- and tri-peptides, whereas the Oligopeptide Transport (OPT) family members import tetra- and pentapeptides. Recently, the novel family of Fungal Oligopeptide Transporters (FOT) has been identified in Saccharomyces cerevisiae wine strains as a result of a horizontal gene transfer from Torulaspora microellipsoides. In natural grape must fermentations with S. cerevisiae, Fots have a broader range of oligopeptide utilization in comparison with non-Fot strains, leading to higher biomass production and better fermentation efficiency. In this review we present the current knowledge on the diversity of oligopeptide transporters in yeast, also discussing how the consumption of oligopeptides provides an adaptive advantage to yeasts within the wine environment.
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Affiliation(s)
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes, Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Département de Biologie, Université Laval, Québec City, QC, Canada
| | - Virginie Galeote
- SPO, INRAE, Université de Montpellier, Montpellier SupAgro, Montpellier, France
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16
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Evaluation of the Fermentative Capacity of Saccharomyces cerevisiae CAT-1 and BB9 Strains and Pichia kudriavzevii BB2 at Simulated Industrial Conditions. Indian J Microbiol 2020; 60:494-504. [PMID: 33087999 DOI: 10.1007/s12088-020-00891-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 01/12/2023] Open
Abstract
The search for promising yeasts that surpass the fermentative capacity of commercial strains, such as Saccharomyces cerevisiae CAT-1, is of great importance for industrial ethanol processes in the world. Two yeasts, Pichia kudriavzevii BB2 and Saccharomyces cerevisiae BB9, were evaluated in comparison to the industrial yeast S. cerevisiae CAT-1. The objective was to evaluate the performance profile of the three studied strains in terms of growth, substrate consumption, and metabolite formation, aiming to determine their behaviour in different media and pH conditions. The results showed that under cultivation conditions simulating the medium used in the industrial process (must at 22° Brix at pH 3.0) the highest ethanol productivity was 0.41 g L-1 h-1 for S. cerevisiae CAT-1, compared to 0.11 g L-1 h-1 and 0.16 g L-1 h-1 for P. kudriavzevii and S. cerevisiae BB2, respectively. S. cerevisiae CAT-1 produced three times more ethanol in must at pH 3.0 (28.30 g L-1) and in mineral medium at pH 3.0 (29.17 g L-1) and 5.0 (30.70 g L-1) when compared to the value obtained in sugarcane must pH 3.0 (9.89 g L-1). It was concluded that S. cerevisiae CAT-1 was not limited by the variation in pH in the mineral medium due to its nutritional composition, guaranteeing better performance of the yeast even in the presence of stressors. Only S. cerevisiae CAT-1 expressed he constitutive invertase enzyme, which is responsible for hydrolysing the sucrose contained in the must.
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17
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Transcriptome analysis reveals the protection mechanism of proanthocyanidins for Saccharomyces cerevisiae during wine fermentation. Sci Rep 2020; 10:6676. [PMID: 32317674 PMCID: PMC7174367 DOI: 10.1038/s41598-020-63631-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/31/2020] [Indexed: 11/08/2022] Open
Abstract
Grape-derived proanthocyanidins could act as a protector against various environmental stresses for Saccharomyces cerevisiae during wine fermentation, resulting in the increased physiological activity, fermentation efficiency and improved wine quality. In order to explore the possible protection mechanism of proanthocyanidins globally, RNA-seq analysis for wine yeast AWRI R2 cultivated with 0 g/L (group A), 0.1 g/L (group B), 1.0 g/L (group C) proanthocyanidins were applied in this study. Differentially expressed genes were enriched into six metabolic pathways including vitamin B6, thiamine, amino acids, aminoacyl-tRNA, carbohydrate and steroid based on KEGG enrichment analysis. Four key genes (SNZ2, THI6, THI21 and THI80), participated in the biosynthesis of vitamin B6 and thiamine, were up-regulated significantly in proanthocyanidins treated yeast cells and the gene expression levels were verified by RT-qPCR. Yeast cells supplemented with proanthocyanidins performed increased intracellular levels of vitamin B6 and thiamine and higher cell viability compared to the control group. In addition, the composition of intracellular fatty acids showed an obvious alternation in proanthocyanidins-treated yeast cells, in which the UFAs content increased whereas the SFA content decreased. In general, we provided an indirect protection effect of proanthocyanidins on the yeast cells to alleviate environmental stresses during wine fermentation.
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18
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Bioprospection of Enzymes and Microorganisms in Insects to Improve Second-Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2019. [DOI: 10.1089/ind.2019.0019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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19
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Walker GM, Basso TO. Mitigating stress in industrial yeasts. Fungal Biol 2019; 124:387-397. [PMID: 32389301 DOI: 10.1016/j.funbio.2019.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/23/2019] [Accepted: 10/25/2019] [Indexed: 01/19/2023]
Abstract
The yeast, Saccharomyces cerevisiae, is the premier fungal cell factory exploited in industrial biotechnology. In particular, ethanol production by yeast fermentation represents the world's foremost biotechnological process, with beverage and fuel ethanol contributing significantly to many countries economic and energy sustainability. During industrial fermentation processes, yeast cells are subjected to several physical, chemical and biological stress factors that can detrimentally affect ethanol yields and overall production efficiency. These stresses include ethanol toxicity, osmostress, nutrient starvation, pH and temperature shock, as well as biotic stress due to contaminating microorganisms. Several cell physiological and genetic approaches to mitigate yeast stress during industrial fermentations can be undertaken, and such approaches will be discussed with reference to stress mitigation in yeasts employed in Brazilian bioethanol processes. This article will highlight the importance of furthering our understanding of key aspects of yeast stress physiology and the beneficial impact this can have more generally on enhancing industrial fungal bioprocesses.
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Affiliation(s)
| | - Thiago O Basso
- Department of Chemical Engineering, Universidade de São Paulo, Brazil.
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20
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Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
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Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
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Lourencetti NMS, Wolf IR, Lacerda MPF, Valente GT, Zanelli CF, Santoni MM, Mendes-Giannini MJS, Enguita FJ, Fusco-Almeida AM. Transcriptional profile of a bioethanol production contaminant Candida tropicalis. AMB Express 2018; 8:166. [PMID: 30311091 PMCID: PMC6182018 DOI: 10.1186/s13568-018-0693-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/26/2022] Open
Abstract
The fermentation process is widely used in the industry for bioethanol production. Even though it is widely used, microbial contamination is unpredictable and difficult to control. The problem of reduced productivity is directly linked to competition for nutrients during contamination. Yeasts representing the Candida species are frequently isolated contaminants. Elucidating the behavior of a contaminant during the fermentation cycle is essential for combatting the contamination. Consequently, the aim of the current study was to better understand the functional and transcriptional behavior of a contaminating yeast Candida tropicalis. We used a global RNA sequencing approach (RNA-seq/MiSeq) to analyze gene expression. Genes with significantly repressed or induced expression, and related to the fermentations process, such as sugar transport, pyruvate decarboxylase, amino acid metabolism, membrane, tolerance to high concentrations of ethanol and temperatures, nutrient suppression), and transcription-linked processes, were identified. The expression pattern suggested that the functional and transcriptional behavior of the contaminating yeast during fermentation for bioethanol production is similar to that of the standard yeast Saccharomyces cerevisiae. In addition, the analysis confirmed that C. tropicalis is an important contaminant of the alcoholic fermentation process, generating bioethanol and viability through its tolerance to all the adversities of a fermentation process essential for the production of bioethanol. According on the gene expression profile, many of these mechanisms are similar to those of S. cerevisiae strains currently used for bioethanol production. These mechanisms can inform studies on antimicrobials, to combat yeast contamination during industrial bioethanol production.
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22
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Paulino de Souza J, Dias do Prado C, Eleutherio EC, Bonatto D, Malavazi I, Ferreira da Cunha A. Improvement of Brazilian bioethanol production – Challenges and perspectives on the identification and genetic modification of new strains of Saccharomyces cerevisiae yeasts isolated during ethanol process. Fungal Biol 2018; 122:583-591. [DOI: 10.1016/j.funbio.2017.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
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23
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Liu ZL, Wang X, Weber SA. Tolerant industrial yeast Saccharomyces cerevisiae posses a more robust cell wall integrity signaling pathway against 2-furaldehyde and 5-(hydroxymethyl)-2-furaldehyde. J Biotechnol 2018; 276-277:15-24. [DOI: 10.1016/j.jbiotec.2018.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/07/2018] [Indexed: 10/17/2022]
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24
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Monteiro B, Ferraz P, Barroca M, da Cruz SH, Collins T, Lucas C. Conditions promoting effective very high gravity sugarcane juice fermentation. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:251. [PMID: 30237826 PMCID: PMC6142328 DOI: 10.1186/s13068-018-1239-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/27/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Applying very high gravity (VHG) fermentation conditions to the sugarcane juice (SCJ) bioethanol industry would improve its environmental and economic sustainability without the need for major infrastructure changes or investments. It could enable a decrease in the consumption of biological and natural resources (cane/land, water and energy) while maintaining acceptable production parameters. The present study attempts to demonstrate and characterise an effective industrially relevant SCJ-VHG fermentation process. RESULTS An industry-like SCJ-VHG bioethanol production process with 30 and 35 °Bx broth was employed to investigate the effects of both the yeast strain used and nitrogen source supplementation on process yield, process productivity, biomass viability, glycerol concentration and retention-associated gene expression. Process performance was shown to be variably affected by the different process conditions investigated. Highest process efficiency, with a 17% (w/v) ethanol yield and only 0.2% (w/v) sugar remaining unfermented, was observed with the Saccharomyces cerevisiae industrial strain CAT-1 in 30 °Bx broth with urea supplementation. In addition, efficient retention of glycerol by the yeast strain was identified as a requisite for better fermentation and was consistent with a higher expression of glycerol permease STL1 and channel FPS1. Urea was shown to promote the deregulation of STL1 expression, overcoming glucose repression. The consistency between Fps1-mediated ethanol secretion and ethanol in the extracellular media reinforces previous suggestions that ethanol might exit the cell through the Fps1 channel. CONCLUSIONS This work brings solid evidence in favour of the utilisation of VHG conditions in SCJ fermentations, bringing it a step closer to industrial application. SCJ concentrated up to 30 °Bx maintains industrially relevant ethanol production yield and productivity, provided the broth is supplemented with a suitable nitrogen source and an appropriate industrial bioethanol-producing yeast strain is used. In addition, the work contributes to a better understanding of the VHG-SCJ process and the variable effects of process parameters on process efficiency and yeast strain response.
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Affiliation(s)
- Bruno Monteiro
- Laboratory of Food and Beverage Biotechnology, ESALQ, University of São Paulo, Piracicaba, SP 13418-900 Brazil
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Ferraz
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Mário Barroca
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sandra H. da Cruz
- Laboratory of Food and Beverage Biotechnology, ESALQ, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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25
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Abstract
Selfishness is pervasive and manifests at all scales of biology, from societies, to individuals, to genetic elements within a genome. The relentless struggle to seek evolutionary advantages drives perpetual cycles of adaptation and counter-adaptation, commonly referred to as Red Queen interactions. In this review, we explore insights gleaned from molecular and genetic studies of such genetic conflicts, both extrinsic (between genomes) and intrinsic (within genomes or cells). We argue that many different characteristics of selfish genetic elements can be distilled into two types of advantages: an over-replication advantage (e.g. mobile genetic elements in genomes) and a transmission distortion advantage (e.g. meiotic drivers in populations). These two general categories may help classify disparate types of selfish genetic elements.
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Affiliation(s)
- Richard N McLaughlin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA .,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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26
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Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain. GENOME ANNOUNCEMENTS 2017; 5:5/13/e00111-17. [PMID: 28360170 PMCID: PMC5374244 DOI: 10.1128/genomea.00111-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we present the draft genome sequence of Saccharomyces cerevisiae BG-1, a Brazilian industrial strain widely used for bioethanol production from sugarcane. The 11.7-Mb genome sequence consists of 216 scaffolds and harbors 5,607 predicted protein-coding genes.
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27
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Weber N, Gorwa-Grauslund M, Carlquist M. Improvement of whole-cell transamination with Saccharomyces cerevisiae using metabolic engineering and cell pre-adaptation. Microb Cell Fact 2017; 16:3. [PMID: 28049528 PMCID: PMC5209827 DOI: 10.1186/s12934-016-0615-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/09/2016] [Indexed: 01/27/2023] Open
Abstract
Background Whole-cell biocatalysis based on metabolically active baker’s yeast with engineered transamination activity can be used to generate molecules carrying a chiral amine moiety. A prerequisite is though to express efficient ω-transaminases and to reach sufficient intracellular precursor levels. Results Herein, the efficiency of three different ω-transaminases originating from Capsicum chinense, Chromobacterium violaceum, and Ochrobactrum anthropi was compared for whole-cell catalyzed kinetic resolution of racemic 1-phenylethylamine to (R)-1-phenylethylamine. The gene from the most promising candidate, C. violaceum ω-transaminase (CV-TA), was expressed in a strain lacking pyruvate decarboxylase activity, which thereby accumulate the co-substrate pyruvate during glucose assimilation. However, the conversion increased only slightly under the applied reaction conditions. In parallel, the effect of increasing the intracellular pyridoxal-5′-phosphate (PLP) level by omission of thiamine during cultivation was investigated. It was found that without thiamine, PLP supplementation was redundant to keep high in vivo transamination activity. Furthermore, higher reaction rates were achieved using a strain containing several copies of CV-TA gene, highlighting the necessity to also increase the intracellular transaminase level. At last, this strain was also investigated for asymmetric whole-cell bioconversion of acetophenone to (S)-1-phenylethylamine using l-alanine as amine donor. Although functionality could be demonstrated, the activity was extremely low indicating that the native co-product removal system was unable to drive the reaction towards the amine under the applied reaction conditions. Conclusions Altogether, our results demonstrate that (R)-1-phenylethylamine with >99% ee can be obtained via kinetic resolution at concentrations above 25 mM racemic substrate with glucose as sole co-substrate when combining appropriate genetic and process engineering approaches. Furthermore, the engineered yeast strain with highest transaminase activity was also shown to be operational as whole-cell catalyst for the production of (S)-1-phenylethylamine via asymmetric transamination of acetophenone, albeit with very low conversion. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0615-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Weber
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden.,Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland
| | - Marie Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden.
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28
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Chen Y, Lu Z, Chen D, Wei Y, Chen X, Huang J, Guan N, Lu Q, Wu R, Huang R. Transcriptomic analysis and driver mutant prioritization for differentially expressed genes from a Saccharomyces cerevisiae strain with high glucose tolerance generated by UV irradiation. RSC Adv 2017. [DOI: 10.1039/c7ra06146c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Driver mutations of a Saccharomyces cerevisiae mutant phenotype strain with high sugar tolerance were sought by the PheNetic network.
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Affiliation(s)
- Ying Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning
- P. R. China
- College of Life Science and Technology
| | - Zhilong Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning
- P. R. China
- College of Life Science and Technology
| | - Dong Chen
- National Engineering Research Center for Non-Food Biorefinery
- Guangxi Academy of Sciences
- Nanning
- P. R. China
| | - Yutuo Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning
- P. R. China
- College of Life Science and Technology
| | - Xiaoling Chen
- National Engineering Research Center for Non-Food Biorefinery
- Guangxi Academy of Sciences
- Nanning
- P. R. China
| | - Jun Huang
- National Engineering Research Center for Non-Food Biorefinery
- Guangxi Academy of Sciences
- Nanning
- P. R. China
| | - Ni Guan
- National Engineering Research Center for Non-Food Biorefinery
- Guangxi Academy of Sciences
- Nanning
- P. R. China
| | - Qi Lu
- National Engineering Research Center for Non-Food Biorefinery
- Guangxi Academy of Sciences
- Nanning
- P. R. China
| | - Renzhi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning
- P. R. China
- College of Life Science and Technology
| | - Ribo Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning
- P. R. China
- College of Life Science and Technology
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29
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Lopes ML, Paulillo SCDL, Godoy A, Cherubin RA, Lorenzi MS, Giometti FHC, Bernardino CD, Amorim Neto HBD, Amorim HVD. Ethanol production in Brazil: a bridge between science and industry. Braz J Microbiol 2016; 47 Suppl 1:64-76. [PMID: 27818090 PMCID: PMC5156502 DOI: 10.1016/j.bjm.2016.10.003] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/05/2016] [Indexed: 12/13/2022] Open
Abstract
In the last 40 years, several scientific and technological advances in microbiology of the fermentation have greatly contributed to evolution of the ethanol industry in Brazil. These contributions have increased our view and comprehension about fermentations in the first and, more recently, second-generation ethanol. Nowadays, new technologies are available to produce ethanol from sugarcane, corn and other feedstocks, reducing the off-season period. Better control of fermentation conditions can reduce the stress conditions for yeast cells and contamination by bacteria and wild yeasts. There are great research opportunities in production processes of the first-generation ethanol regarding high-value added products, cost reduction and selection of new industrial yeast strains that are more robust and customized for each distillery. New technologies have also focused on the reduction of vinasse volumes by increasing the ethanol concentrations in wine during fermentation. Moreover, conversion of sugarcane biomass into fermentable sugars for second-generation ethanol production is a promising alternative to meet future demands of biofuel production in the country. However, building a bridge between science and industry requires investments in research, development and transfer of new technologies to the industry as well as specialized personnel to deal with new technological challenges.
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30
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Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation. G3-GENES GENOMES GENETICS 2016; 6:2421-34. [PMID: 27317778 PMCID: PMC4978896 DOI: 10.1534/g3.116.029397] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker's/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation.
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Genetic Enhancement of Saccharomyces cerevisiae for First and Second Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1201/b19347-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. G3-GENES GENOMES GENETICS 2016; 6:1757-66. [PMID: 27172212 PMCID: PMC4889671 DOI: 10.1534/g3.116.029389] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.
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Marsit S, Sanchez I, Galeote V, Dequin S. Horizontally acquired oligopeptide transporters favour adaptation ofSaccharomyces cerevisiaewine yeast to oenological environment. Environ Microbiol 2016; 18:1148-61. [DOI: 10.1111/1462-2920.13117] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Souhir Marsit
- INRA; UMR1083 Sciences pour l'Oenology; Montpellier France
| | | | | | - Sylvie Dequin
- INRA; UMR1083 Sciences pour l'Oenology; Montpellier France
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Marques WL, Raghavendran V, Stambuk BU, Gombert AK. Sucrose and Saccharomyces cerevisiae: a relationship most sweet. FEMS Yeast Res 2015; 16:fov107. [PMID: 26658003 DOI: 10.1093/femsyr/fov107] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 12/16/2022] Open
Abstract
Sucrose is an abundant, readily available and inexpensive substrate for industrial biotechnology processes and its use is demonstrated with much success in the production of fuel ethanol in Brazil. Saccharomyces cerevisiae, which naturally evolved to efficiently consume sugars such as sucrose, is one of the most important cell factories due to its robustness, stress tolerance, genetic accessibility, simple nutrient requirements and long history as an industrial workhorse. This minireview is focused on sucrose metabolism in S. cerevisiae, a rather unexplored subject in the scientific literature. An analysis of sucrose availability in nature and yeast sugar metabolism was performed, in order to understand the molecular background that makes S. cerevisiae consume this sugar efficiently. A historical overview on the use of sucrose and S. cerevisiae by humans is also presented considering sugarcane and sugarbeet as the main sources of this carbohydrate. Physiological aspects of sucrose consumption are compared with those concerning other economically relevant sugars. Also, metabolic engineering efforts to alter sucrose catabolism are presented in a chronological manner. In spite of its extensive use in yeast-based industries, a lot of basic and applied research on sucrose metabolism is imperative, mainly in fields such as genetics, physiology and metabolic engineering.
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Affiliation(s)
- Wesley Leoricy Marques
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
| | | | - Boris Ugarte Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis-SC, 88040-900, Brazil
| | - Andreas Karoly Gombert
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
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35
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Anoop V, Rotaru S, Shwed PS, Tayabali AF, Arvanitakis G. Review of current methods for characterizing virulence and pathogenicity potential of industrial Saccharomyces cerevisiae strains towards humans. FEMS Yeast Res 2015. [PMID: 26195617 DOI: 10.1093/femsyr/fov057] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Most industrial Saccharomyces cerevisiae strains used in food or biotechnology processes are benign. However, reports of S. cerevisiae infections have emerged and novel strains continue to be developed. In order to develop recommendations for the human health risk assessment of S. cerevisiae strains, we conducted a literature review of current methods used to characterize their pathogenic potential and evaluated their relevance towards risk assessment. These studies revealed that expression of virulence traits in S. cerevisiae is complex and depends on many factors. Given the opportunistic nature of this organism, an approach using multiple lines of evidence is likely necessary for the reasonable prediction of the pathogenic potential of a particular strain. Risk assessment of S. cerevisiae strains would benefit from more research towards the comparison of virulent and non-virulent strains in order to better understand those genotypic and phenotypic traits most likely to be associated with pathogenicity.
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Affiliation(s)
- Valar Anoop
- New Substances Assessment and Control Bureau, Safe Environments Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 99 Metcalfe Street, Floor-11, Ottawa, ON K1A 0K9, Canada
| | - Sever Rotaru
- New Substances Assessment and Control Bureau, Safe Environments Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 99 Metcalfe Street, Floor-11, Ottawa, ON K1A 0K9, Canada
| | - Philip S Shwed
- Environmental Health Science Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Colombine Driveway, Ottawa, ON K1A0K9, Canada
| | - Azam F Tayabali
- Environmental Health Science Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Colombine Driveway, Ottawa, ON K1A0K9, Canada
| | - George Arvanitakis
- New Substances Assessment and Control Bureau, Safe Environments Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 99 Metcalfe Street, Floor-11, Ottawa, ON K1A 0K9, Canada
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Tosin C, Andrietta SR, Andrietta MDGS. Population dynamics of yeasts inhabiting bioethanol production with cell recycling. JOURNAL OF THE INSTITUTE OF BREWING 2015. [DOI: 10.1002/jib.237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Saunders LP, Bowman MJ, Mertens JA, Da Silva NA, Hector RE. Triacetic acid lactone production in industrial Saccharomyces yeast strains. ACTA ACUST UNITED AC 2015; 42:711-21. [DOI: 10.1007/s10295-015-1596-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Abstract
Triacetic acid lactone (TAL) is a potential platform chemical that can be produced in yeast. To evaluate the potential for industrial yeast strains to produce TAL, the g2ps1 gene encoding 2-pyrone synthase was transformed into 13 industrial yeast strains of varied genetic background. TAL production varied 63-fold between strains when compared in batch culture with glucose. Ethanol, acetate, and glycerol were also tested as potential carbon sources. Batch cultures with ethanol medium produced the highest titers. Therefore, fed-batch cultivation with ethanol feed was assayed for TAL production in bioreactors, producing our highest TAL titer, 5.2 g/L. Higher feed rates resulted in a loss of TAL and subsequent production of additional TAL side products. Finally, TAL efflux was measured and TAL is actively exported from S. cerevisiae cells. Percent yield for all strains was low, indicating that further metabolic engineering of the strains is required.
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Affiliation(s)
- Lauren P Saunders
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
| | - Michael J Bowman
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
| | - Jeffrey A Mertens
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
| | - Nancy A Da Silva
- grid.266093.8 0000000106687243 Department of Chemical Engineering and Materials Science University of California 92697 Irvine CA USA
| | - Ronald E Hector
- grid.417548.b 0000000404786311 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service U.S. Department of Agriculture 1815 North University Street 61604 Peoria IL USA
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Carvalho-Netto OV, Carazzolle MF, Mofatto LS, Teixeira PJPL, Noronha MF, Calderón LAL, Mieczkowski PA, Argueso JL, Pereira GAG. Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production. Microb Cell Fact 2015; 14:13. [PMID: 25633848 PMCID: PMC4318157 DOI: 10.1186/s12934-015-0196-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 01/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The bioethanol production system used in Brazil is based on the fermentation of sucrose from sugarcane feedstock by highly adapted strains of the yeast Saccharomyces cerevisiae. Bacterial contaminants present in the distillery environment often produce yeast-bacteria cellular co-aggregation particles that resemble yeast-yeast cell adhesion (flocculation). The formation of such particles is undesirable because it slows the fermentation kinetics and reduces the overall bioethanol yield. RESULTS In this study, we investigated the molecular physiology of one of the main S. cerevisiae strains used in Brazilian bioethanol production, PE-2, under two contrasting conditions: typical fermentation, when most yeast cells are in suspension, and co-aggregated fermentation. The transcriptional profile of PE-2 was assessed by RNA-seq during industrial scale fed-batch fermentation. Comparative analysis between the two conditions revealed transcriptional profiles that were differentiated primarily by a deep gene repression in the co-aggregated samples. The data also indicated that Lactobacillus fermentum was likely the main bacterial species responsible for cellular co-aggregation and for the high levels of organic acids detected in the samples. CONCLUSIONS Here, we report the high-resolution gene expression profiling of strain PE-2 during industrial-scale fermentations and the transcriptional reprograming observed under co-aggregation conditions. This dataset constitutes an important resource that can provide support for further development of this key yeast biocatalyst.
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Affiliation(s)
- Osmar V Carvalho-Netto
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Marcelo F Carazzolle
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
| | - Luciana S Mofatto
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
| | - Paulo J P L Teixeira
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
| | - Melline F Noronha
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
| | - Luige A L Calderón
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
| | | | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Gonçalo A G Pereira
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
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39
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Genomic reconstruction to improve bioethanol and ergosterol production of industrial yeast Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2014; 42:207-18. [PMID: 25475753 DOI: 10.1007/s10295-014-1556-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
Baker's yeast (Saccharomyces cerevisiae) is the common yeast used in the fields of bread making, brewing, and bioethanol production. Growth rate, stress tolerance, ethanol titer, and byproducts yields are some of the most important agronomic traits of S. cerevisiae for industrial applications. Here, we developed a novel method of constructing S. cerevisiae strains for co-producing bioethanol and ergosterol. The genome of an industrial S. cerevisiae strain, ZTW1, was first reconstructed through treatment with an antimitotic drug followed by sporulation and hybridization. A total of 140 mutants were selected for ethanol fermentation testing, and a significant positive correlation between ergosterol content and ethanol production was observed. The highest performing mutant, ZG27, produced 7.9 % more ethanol and 43.2 % more ergosterol than ZTW1 at the end of fermentation. Chromosomal karyotyping and proteome analysis of ZG27 and ZTW1 suggested that this breeding strategy caused large-scale genome structural variations and global gene expression diversities in the mutants. Genetic manipulation further demonstrated that the altered expression activity of some genes (such as ERG1, ERG9, and ERG11) involved in ergosterol synthesis partly explained the trait improvement in ZG27.
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40
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Winkler JD, Kao KC. Recent advances in the evolutionary engineering of industrial biocatalysts. Genomics 2014; 104:406-11. [DOI: 10.1016/j.ygeno.2014.09.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 11/15/2022]
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41
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Genomic and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae. Sci Rep 2014; 4:6556. [PMID: 25296911 PMCID: PMC4190571 DOI: 10.1038/srep06556] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/10/2014] [Indexed: 12/15/2022] Open
Abstract
The industrial yeast Saccharomyces cerevisiae is a traditional ethanologenic agent and a promising biocatalyst for advanced biofuels production using lignocellulose materials. Here we present the genomic background of type strain NRRL Y-12632 and its transcriptomic response to 5-hydroxymethyl-2-furaldehyde (HMF), a commonly encountered toxic compound liberated from lignocellulosic-biomass pretreatment, in dissecting the genomic mechanisms of yeast tolerance. Compared with the genome of laboratory model strain S288C, we identified more than 32,000 SNPs in Y-12632 with 23,000 missense and nonsense SNPs. Enriched sequence mutations occurred for genes involved in MAPK- and phosphatidylinositol (PI)- signaling pathways in strain Y-12632, with 41 and 13 genes containing non-synonymous SNPs, respectively. Many of these mutated genes displayed consistent up-regulated signature expressions in response to challenges of 30 mM HMF. Analogous single-gene deletion mutations of these genes showed significantly sensitive growth response on a synthetic medium containing 20 mM HMF. Our results suggest at least three MAPK-signaling pathways, especially for the cell-wall integrity pathway, and PI-signaling pathways to be involved in mediation of yeast tolerance against HMF in industrial yeast Saccharomyces cerevisiae. Higher levels of sequence variations were also observed for genes involved in purine and pyrimidine metabolism pathways.
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42
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Stambuk BU. Biotechnology strategies with industrial fuel ethanol Saccharomyces cerevisiae strains for efficient 1st and 2nd generation bioethanol production from sugarcane. BMC Proc 2014. [PMCID: PMC4204079 DOI: 10.1186/1753-6561-8-s4-o36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Steensels J, Verstrepen KJ. Taming Wild Yeast: Potential of Conventional and Nonconventional Yeasts in Industrial Fermentations. Annu Rev Microbiol 2014; 68:61-80. [DOI: 10.1146/annurev-micro-091213-113025] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium; ,
- Laboratory for Systems Biology, VIB, Bio-Incubator, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium; ,
- Laboratory for Systems Biology, VIB, Bio-Incubator, 3001 Leuven, Belgium
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Comparative genomic analysis of Saccharomyces cerevisiae yeasts isolated from fermentations of traditional beverages unveils different adaptive strategies. Int J Food Microbiol 2014; 171:129-35. [DOI: 10.1016/j.ijfoodmicro.2013.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/11/2013] [Accepted: 10/27/2013] [Indexed: 11/17/2022]
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45
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Abreu-Cavalheiro A, Monteiro G. Solving ethanol production problems with genetically modified yeast strains. Braz J Microbiol 2014; 44:665-71. [PMID: 24516432 PMCID: PMC3910172 DOI: 10.1590/s1517-83822013000300001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 04/01/2013] [Indexed: 11/22/2022] Open
Abstract
The current world demand for bioethanol is increasing as a consequence of low fossil fuel availability and a growing number of ethanol/gasoline flex-fuel cars. In addition, countries in several parts of the world have agreed to reduce carbon dioxide emissions, and the use of ethanol as a fuel (which produces fewer pollutants than petroleum products) has been considered to be a good alternative to petroleum products. The ethanol that is produced in Brazil from the first-generation process is optimized and can be accomplished at low cost. However, because of the large volume of ethanol that is produced and traded each year, any small improvement in the process could represent a savings of billions dollars. Several Brazilian research programs are investing in sugarcane improvement, but little attention has been given to the improvement of yeast strains that participate in the first-generation process at present. The Brazilian ethanol production process uses sugarcane as a carbon source for the yeast Saccharomyces cerevisiae. Yeast is then grown at a high cellular density and high temperatures in large-capacity open tanks with cells recycle. All of these culture conditions compel the yeast to cope with several types of stress. Among the main stressors are high temperatures and high ethanol concentrations inside the fermentation tanks during alcohol production. Moreover, the competition between the desired yeast strains, which are inoculated at the beginning of the process, with contaminants such as wild type yeasts and bacteria, requires acid treatment to successfully recycle the cells. This review is focused on describing the problems and stressors within the Brazilian ethanol production system. It also highlights some genetic modifications that can help to circumvent these difficulties in yeast.
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Affiliation(s)
- A Abreu-Cavalheiro
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - G Monteiro
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
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Zheng DQ, Chen J, Zhang K, Gao KH, Li O, Wang PM, Zhang XY, Du FG, Sun PY, Qu AM, Wu S, Wu XC. Genomic structural variations contribute to trait improvement during whole-genome shuffling of yeast. Appl Microbiol Biotechnol 2013; 98:3059-70. [PMID: 24346281 DOI: 10.1007/s00253-013-5423-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 11/24/2022]
Abstract
Whole-genome shuffling (WGS) is a powerful technology of improving the complex traits of many microorganisms. However, the molecular mechanisms underlying the altered phenotypes in isolates were less clarified. Isolates with significantly enhanced stress tolerance and ethanol titer under very-high-gravity conditions were obtained after WGS of the bioethanol Saccharomyces cerevisiae strain ZTW1. Karyotype analysis and RT-qPCR showed that chromosomal rearrangement occurred frequently in genome shuffling. Thus, the phenotypic effects of genomic structural variations were determined in this study. RNA-Seq and physiological analyses revealed the diverse transcription pattern and physiological status of the isolate S3-110 and ZTW1. Our observations suggest that the improved stress tolerance of S3-110 can be largely attributed to the copy number variations in large DNA regions, which would adjust the ploidy of yeast cells and expression levels of certain genes involved in stress response. Overall, this work not only constructed shuffled S. cerevisiae strains that have potential industrial applications but also provided novel insights into the molecular mechanisms of WGS and enhanced our knowledge on this useful breeding strategy.
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Affiliation(s)
- Dao-Qiong Zheng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
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Homo- and heterofermentative lactobacilli differently affect sugarcane-based fuel ethanol fermentation. Antonie van Leeuwenhoek 2013; 105:169-77. [DOI: 10.1007/s10482-013-0063-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
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48
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Stress tolerance and growth physiology of yeast strains from the Brazilian fuel ethanol industry. Antonie van Leeuwenhoek 2013; 104:1083-95. [DOI: 10.1007/s10482-013-0030-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
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49
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Antonangelo ATBF, Alonso DP, Ribolla PEM, Colombi D. Microsatellite marker-based assessment of the biodiversity of native bioethanol yeast strains. Yeast 2013; 30:307-17. [DOI: 10.1002/yea.2964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ana Teresa B. F. Antonangelo
- Laboratório de Pesquisas e Análises Genéticas (PANGENE), Depto de Parasitologia; IBB-UNESP; Botucatu; SP; Brazil
| | - Diego P. Alonso
- Laboratório de Pesquisas e Análises Genéticas (PANGENE), Depto de Parasitologia; IBB-UNESP; Botucatu; SP; Brazil
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50
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Hector RE, Dien BS, Cotta MA, Mertens JA. Growth and fermentation of D-xylose by Saccharomyces cerevisiae expressing a novel D-xylose isomerase originating from the bacterium Prevotella ruminicola TC2-24. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:84. [PMID: 23721368 PMCID: PMC3673840 DOI: 10.1186/1754-6834-6-84] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/22/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae strains expressing D-xylose isomerase (XI) produce some of the highest reported ethanol yields from D-xylose. Unfortunately, most bacterial XIs that have been expressed in S. cerevisiae are either not functional, require additional strain modification, or have low affinity for D-xylose. This study analyzed several XIs from rumen and intestinal microorganisms to identify enzymes with improved properties for engineering S. cerevisiae for D-xylose fermentation. RESULTS Four XIs originating from rumen and intestinal bacteria were isolated and expressed in a S. cerevisiae CEN.PK2-1C parental strain primed for D-xylose metabolism by over expression of its native D-xylulokinase. Three of the XIs were functional in S. cerevisiae, based on the strain's ability to grow in D-xylose medium. The most promising strain, expressing the XI mined from Prevotella ruminicola TC2-24, was further adapted for aerobic and fermentative growth by serial transfers of D-xylose cultures under aerobic, and followed by microaerobic conditions. The evolved strain had a specific growth rate of 0.23 h-1 on D-xylose medium, which is comparable to the best reported results for analogous S. cerevisiae strains including those expressing the Piromyces sp. E2 XI. When used to ferment D-xylose, the adapted strain produced 13.6 g/L ethanol in 91 h with a metabolic yield of 83% of theoretical. From analysis of the P. ruminicola XI, it was determined the enzyme possessed a Vmax of 0.81 μmole/min/mg protein and a Km of 34 mM. CONCLUSION This study identifies a new xylose isomerase from the rumen bacterium Prevotella ruminicola TC2-24 that has one of the highest affinities and specific activities compared to other bacterial and fungal D-xylose isomerases expressed in yeast. When expressed in S. cerevisiae and used to ferment D-xylose, very high ethanol yield was obtained. This new XI should be a promising resource for constructing other D-xylose fermenting strains, including industrial yeast genetic backgrounds.
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Affiliation(s)
- Ronald E Hector
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
| | - Bruce S Dien
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
| | - Michael A Cotta
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
| | - Jeffrey A Mertens
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
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