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Salas-Navarrete PC, de Oca Miranda AIM, Martínez A, Caspeta L. Evolutionary and reverse engineering to increase Saccharomyces cerevisiae tolerance to acetic acid, acidic pH, and high temperature. Appl Microbiol Biotechnol 2021; 106:383-399. [PMID: 34913993 DOI: 10.1007/s00253-021-11730-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/24/2022]
Abstract
Saccharomyces cerevisiae scarcely grows on minimal media with acetic acid, acidic pH, and high temperatures. In this study, the adaptive laboratory evolution (ALE), whole-genome analysis, and reverse engineering approaches were used to generate strains tolerant to these conditions. The thermotolerant strain TTY23 and its parental S288C were evolved through 1 year, in increasing concentrations of acetic acid up to 12 g/L, keeping the pH ≤ 4. Of the 18 isolated strains, 9 from each ancestor, we selected the thermo-acid tolerant TAT12, derived from TTY23, and the acid tolerant AT22, derived from S288C. Both grew in minimal media with 12 g/L of acetic acid, pH 4, and 30 °C, and produced ethanol up to 29.25 ± 6 mmol/gDCW/h-neither of the ancestors thrived in these conditions. Furthermore, only the TAT12 grew on 2 g/L of acetic acid, pH 3, and 37 °C, and accumulated 16.5 ± 0.5 mmol/gDCW/h of ethanol. Whole-genome sequencing and transcriptomic analysis of this strain showed changes in the genetic sequence and transcription of key genes involved in the RAS-cAMP-PKA signaling pathway (RAS2, GPA2, and IRA2), the heat shock transcription factor (HSF1), and the positive regulator of replication initiation (SUM1), among others. By reverse engineering, the relevance of the combined mutations in the genes RAS2, HSF1, and SUM1 to the tolerance for acetic acid, low pH, and high temperature was confirmed. Alone, the RAS2 mutation yielded acid tolerance and HSF1 nutation thermotolerance. Increasing the thermo-acidic niche and acetic acid tolerance of S. cerevisiae can contribute to improve economic ethanol production. KEY POINTS: • Thermo-acid tolerant (TAT) yeast strains were generated by adaptive laboratory evolution. • The strain TAT12 thrived on non-native, thermo-acidic harmful conditions. • Mutations in RAS2, HSF1, and SUM1 genes rendered yeast thermo and acid tolerant.
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Affiliation(s)
- Prisciluis Caheri Salas-Navarrete
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, Mexico
| | - Arturo Iván Montes de Oca Miranda
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, Mexico
| | - Alfredo Martínez
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, C.P. 62210, Cuernavaca, Morelos, Mexico
| | - Luis Caspeta
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, C.P. 62210, Cuernavaca, Morelos, Mexico.
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Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate. G3-GENES GENOMES GENETICS 2020; 10:1375-1391. [PMID: 32086247 PMCID: PMC7144085 DOI: 10.1534/g3.119.400986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Schizosaccharomyces pombe is a model unicellular eukaryote with ties to the basic research, oenology and industrial biotechnology sectors. While most investigations into S. pombe cell biology utilize Leupold’s 972h- laboratory strain background, recent studies have described a wealth of genetic and phenotypic diversity within wild populations of S. pombe including stress resistance phenotypes which may be of interest to industry. Here we describe the genomic and transcriptomic characterization of Wilmar-P, an S. pombe isolate used for bioethanol production from sugarcane molasses at industrial scale. Novel sequences present in Wilmar-P but not in the laboratory S. pombe genome included multiple coding sequences with near-perfect nucleotide identity to Schizosaccharomyces octosporus sequences. Wilmar-P also contained a ∼100kb duplication in the right arm of chromosome III, a region harboring ght5+, the predominant hexose transporter encoding gene. Transcriptomic analysis of Wilmar-P grown in molasses revealed strong downregulation of core environmental stress response genes and upregulation of hexose transporters and drug efflux pumps compared to laboratory S. pombe. Finally, examination of the regulatory network of Scr1, which is involved in the regulation of several genes differentially expressed on molasses, revealed expanded binding of this transcription factor in Wilmar-P compared to laboratory S. pombe in the molasses condition. Together our results point to both genomic plasticity and transcriptomic adaptation as mechanisms driving phenotypic adaptation of Wilmar-P to the molasses environment and therefore adds to our understanding of genetic diversity within industrial fission yeast strains and the capacity of this strain for commercial scale bioethanol production.
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Cunha JT, Costa CE, Ferraz L, Romaní A, Johansson B, Sá-Correia I, Domingues L. HAA1 and PRS3 overexpression boosts yeast tolerance towards acetic acid improving xylose or glucose consumption: unravelling the underlying mechanisms. Appl Microbiol Biotechnol 2018; 102:4589-4600. [PMID: 29607452 DOI: 10.1007/s00253-018-8955-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 11/28/2022]
Abstract
Acetic acid tolerance and xylose consumption are desirable traits for yeast strains used in industrial biotechnological processes. In this work, overexpression of a weak acid stress transcriptional activator encoded by the gene HAA1 and a phosphoribosyl pyrophosphate synthetase encoded by PRS3 in a recombinant industrial Saccharomyces cerevisiae strain containing a xylose metabolic pathway was evaluated in the presence of acetic acid in xylose- or glucose-containing media. HAA1 or PRS3 overexpression resulted in superior yeast growth and higher sugar consumption capacities in the presence of 4 g/L acetic acid, and a positive synergistic effect resulted from the simultaneous overexpression of both genes. Overexpressing these genes also improved yeast adaptation to a non-detoxified hardwood hydrolysate with a high acetic acid content. Furthermore, the overexpression of HAA1 and/or PRS3 was found to increase the robustness of yeast cell wall when challenged with acetic acid stress, suggesting the involvement of the modulation of the cell wall integrity pathway. This study clearly shows HAA1 and/or, for the first time, PRS3 overexpression to play an important role in the improvement of industrial yeast tolerance towards acetic acid. The results expand the molecular toolbox and add to the current understanding of the mechanisms involved in higher acetic acid tolerance, paving the way for the further development of more efficient industrial processes.
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Affiliation(s)
- Joana T Cunha
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carlos E Costa
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luís Ferraz
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Aloia Romaní
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Björn Johansson
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Chen L, Zhang YH, Huang T, Cai YD. Gene expression profiling gut microbiota in different races of humans. Sci Rep 2016; 6:23075. [PMID: 26975620 PMCID: PMC4791684 DOI: 10.1038/srep23075] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment, and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.,College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China
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Cui FX, Zhang RM, Liu HQ, Wang YF, Li H. Metabolic responses to Lactobacillus plantarum contamination or bacteriophage treatment in Saccharomyces cerevisiae using a GC–MS-based metabolomics approach. World J Microbiol Biotechnol 2015; 31:2003-13. [DOI: 10.1007/s11274-015-1949-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 09/15/2015] [Indexed: 12/01/2022]
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Barth D, de Souza Monteiro AR, da Costa MM, Virkajärvi I, Sacon V, Wilhelmsom A. DesinFix TM 135 in fermentation process for bioethanol production. Braz J Microbiol 2014; 45:323-5. [PMID: 24948951 PMCID: PMC4059317 DOI: 10.1590/s1517-83822014000100046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
Brazil has the world’s largest ethanol production from sugarcane, but bacterial contamination decreases the ethanol yields. It was shown that the biocide DesinFix™ 135 can reduce the contamination without decreasing the yeasts’ viability or negatively affecting the ethanol production.
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An organic acid-tolerant HAA1-overexpression mutant of an industrial bioethanol strain of Saccharomyces cerevisiae and its application to the production of bioethanol from sugarcane molasses. AMB Express 2013; 3:74. [PMID: 24373204 PMCID: PMC3896689 DOI: 10.1186/2191-0855-3-74] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022] Open
Abstract
Bacterial contamination is known as a major cause of the reduction in ethanol yield during bioethanol production by Saccharomyces cerevisiae. Acetate is an effective agent for the prevention of bacterial contamination, but it negatively affects the fermentation ability of S. cerevisiae. We have proposed that the combined use of organic acids including acetate and lactate and yeast strains tolerant to organic acids may be effective for the elimination of principally lactic acid bacterial (LAB) contamination. In a previous study employing laboratory S. cerevisiae strains, we showed that overexpression of the HAA1 gene, which encodes a transcriptional activator, could be a useful molecular breeding method for acetate-tolerant yeast strains. In the present study, we constructed a HAA1-overexpressing diploid strain (MATa/α, named ER HAA1-OP) derived from the industrial bioethanol strain Ethanol Red (ER). ER HAA1-OP showed tolerance not only to acetate but also to lactate, and this tolerance was dependent on the increased expression of HAA1 gene. The ethanol production ability of ER HAA1-OP was almost equivalent to that of the parent strain during the bioethanol production process from sugarcane molasses in the absence of acetate. The addition of acetate at 0.5% (w/v, pH 4.5) inhibited the fermentation ability of the parent strain, but such an inhibition was not observed in the ethanol production process using ER HAA1-OP.
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Enhancement of acetic acid tolerance in Saccharomyces cerevisiae by overexpression of the HAA1 gene, encoding a transcriptional activator. Appl Environ Microbiol 2012; 78:8161-3. [PMID: 22961896 DOI: 10.1128/aem.02356-12] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Haa1 is a transcriptional activator required for Saccharomyces cerevisiae adaptation to weak acids. Here we show that the constitutive HAA1-overexpressing strain acquired a higher level of acetic acid tolerance. Under conditions of acetic acid stress, the intracellular level of acetic acid was significantly lower in HAA1-overexpressing cells than in the wild-type cells.
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Haitani Y, Tanaka K, Yamamoto M, Nakamura T, Ando A, Ogawa J, Shima J. Identification of an acetate-tolerant strain of Saccharomyces cerevisiae and characterization by gene expression analysis. J Biosci Bioeng 2012; 114:648-51. [PMID: 22841865 DOI: 10.1016/j.jbiosc.2012.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/02/2012] [Accepted: 07/04/2012] [Indexed: 11/18/2022]
Abstract
A massive screening was performed to identify an acetate-tolerant strain of Saccharomyces cerevisiae. We found that S. cerevisiae ATCC 38555 is acetate-tolerant, with a fermentation profile indicating that it has a high level of acetate adaptation. The global gene expression analysis indicated that AFT1- and HAA1-regulated genes are clearly up-regulated.
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Affiliation(s)
- Yutaka Haitani
- Research Division of Microbial Sciences, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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Gattlen J, Zinn M, Guimond S, Körner E, Amberg C, Mauclaire L. Biofilm formation by the yeast Rhodotorula mucilaginosa: process, repeatability and cell attachment in a continuous biofilm reactor. BIOFOULING 2011; 27:979-991. [PMID: 21981116 DOI: 10.1080/08927014.2011.619657] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Yeast biofilms contribute to quality impairment of industrial processes and also play an important role in clinical infections. Little is known about biofilm formation and their treatment. The aim of this study was to establish a multi-layer yeast biofilm model using a modified 3.7 l bench-top bioreactor operated in continuous mode (D = 0.12 h(-1)). The repeatability of biofilm formation was tested by comparing five bioprocesses with Rhodotorula mucilaginosa, a strain isolated from washing machines. The amount of biofilm formed after 6 days post inoculation was 83 μg cm(-2) protein, 197 μg cm(-2) polysaccharide and 6.9 × 10(6) CFU cm(-2) on smooth polypropylene surfaces. Roughening the surface doubled the amount of biofilm but also increased its spatial variability. Plasma modification of polypropylene significantly reduced the hydrophobicity but did not enhance cell attachment. The biofilm formed on polypropylene coupons could be used for sanitation studies.
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Affiliation(s)
- Jasmin Gattlen
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomaterials, Lerchenfeldstrasse 5, CH-9014, St. Gallen, Switzerland
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Katakura Y, Moukamnerd C, Harashima S, Kino-oka M. Strategy for preventing bacterial contamination by adding exogenous ethanol in solid-state semi-continuous bioethanol production. J Biosci Bioeng 2011; 111:343-5. [DOI: 10.1016/j.jbiosc.2010.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/01/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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