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Branduardi P, Barroso L, Dato L, Louis EJ, Porro D. Molecular Tools for Leveraging the Potential of the Acid-Tolerant Yeast Zygosaccharomyces bailii as Cell Factory. Methods Mol Biol 2022; 2513:179-204. [PMID: 35781206 DOI: 10.1007/978-1-0716-2399-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microorganisms offer a tremendous potential as cell factories, and they are indeed been used by humans since the previous centuries for biotransformations. Among them, yeasts combine the advantage of a unicellular state with a eukaryotic organization. Moreover, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycete budding yeast, is widely known for its peculiar tolerance to different stresses, among which are organic acids. Moreover, the recent reclassification of the species, including diverse hybrids, is further expanding both fundamental and applied interests. It is therefore reasonable that despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here we describe in detail the methods for determining chromosome number, size, and aneuploidy, transformation, classical target gene disruption or gene integration, and designing of episomal expression plasmids helpful for engineering the yeast Z. bailii .
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Affiliation(s)
- Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
| | - Liliane Barroso
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Laura Dato
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Edward J Louis
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Tanaka K, Miyata H, Sugimura K, Fukuda S, Kanemura T, Yamashita K, Miyazaki Y, Takahashi T, Kurokawa Y, Yamasaki M, Wada H, Nakajima K, Takiguchi S, Mori M, Doki Y. miR-27 is associated with chemoresistance in esophageal cancer through transformation of normal fibroblasts to cancer-associated fibroblasts. Carcinogenesis 2015; 36:894-903. [PMID: 26026166 DOI: 10.1093/carcin/bgv067] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 04/20/2015] [Indexed: 02/07/2023] Open
Abstract
There is increasing evidence that the expression of microRNA (miRNA) in cancer is associated with chemosensitivity but the mechanism of miRNA-induced chemoresistance has not been fully elucidated. The aim of this study was to examine the role of extracellular miRNA in the response to chemotherapy in esophageal cancer. First, serum expression of miRNAs selected by miRNA array was measured by quantitative reverse transcription-polymerase chain reaction in 68 patients with esophageal cancer who received cisplatin-based chemotherapy to examine the relationship between miRNA expression and response to chemotherapy. The serum expression levels of 18 miRNAs were different between responders and non-responders by miRNA array. Of these, high expression levels of miR-27a/b correlated with poor response to chemotherapy in patients with esophageal cancer. Next, in vitro assays were conducted to investigate the mechanism of miRNA-induced chemoresistance. Although transfection of miR-27a/b to cancer cells had no significant impact on chemosensitivity, esophageal cancer cells cultured in supernatant of miR-27a/b-transfected normal fibroblast showed reduced chemosensitivity to cisplatin, compared with cancer cells cultured in supernatant of normal fibroblast. MiR-27a/b-transfected normal fibroblast showed α-smooth muscle actin (α-SMA) expression, a marker of cancer-associated fibroblasts (CAF) and increased production of transforming growth factor-β (TGF-β). Chemosensitivity recovered after administration of neutralizing antibody of TGF-β to the supernatant transfer experiments. Our results indicated that miR-27a/b is involved in resistance to chemotherapy in esophageal cancer, through miR-27a/b-induced transformation of normal fibroblast into CAF.
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Affiliation(s)
- Koji Tanaka
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Hiroshi Miyata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Keijiro Sugimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Shuichi Fukuda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Takashi Kanemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Kotaro Yamashita
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Yasuhiro Miyazaki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Tsuyoshi Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Yukinori Kurokawa
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Makoto Yamasaki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Hisashi Wada
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Kiyokazu Nakajima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Shuji Takiguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita city, Osaka 565-0871, Japan
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Branduardi P, Dato L, Porro D. Molecular tools and protocols for engineering the acid-tolerant yeast Zygosaccharomyces bailii as a potential cell factory. Methods Mol Biol 2014; 1152:63-85. [PMID: 24744027 DOI: 10.1007/978-1-4939-0563-8_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microorganisms offer a tremendous potential as cell factories, and they are indeed used by humans for centuries for biotransformations. Among them, yeasts combine the advantage of unicellular state with a eukaryotic organization, and, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycetales budding yeast, is widely known for its peculiar tolerance to various stresses, among which are organic acids. Despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here, we describe in detail protocols for transformation, for target gene disruption or gene integration, and for designing episomal expression plasmids helpful for developing and further studying the yeast Z. bailii.
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Affiliation(s)
- Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2 - 20126, Milan, Italy,
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Efficient expression and purification of recombinant alcohol oxidase in Pichia pastoris. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-011-0660-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Oliveira C, Guimarães PM, Domingues L. Recombinant microbial systems for improved β-galactosidase production and biotechnological applications. Biotechnol Adv 2011; 29:600-9. [DOI: 10.1016/j.biotechadv.2011.03.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/24/2011] [Accepted: 03/31/2011] [Indexed: 11/28/2022]
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Dato L, Branduardi P, Passolunghi S, Cattaneo D, Riboldi L, Frascotti G, Valli M, Porro D. Advances in molecular tools for the use of Zygosaccharomyces bailii as host for biotechnological productions and construction of the first auxotrophic mutant. FEMS Yeast Res 2010; 10:894-908. [DOI: 10.1111/j.1567-1364.2010.00668.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Domingues L, Guimarães PMR, Oliveira C. Metabolic engineering of Saccharomyces cerevisiae for lactose/whey fermentation. Bioeng Bugs 2009; 1:164-71. [PMID: 21326922 DOI: 10.4161/bbug.1.3.10619] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 11/19/2022] Open
Abstract
Lactose is an interesting carbon source for the production of several bio-products by fermentation, primarily because it is the major component of cheese whey, the main by-product of dairy activities. However, the microorganism more widely used in industrial fermentation processes, the yeast Saccharomyces cerevisiae, does not have a lactose metabolization system. Therefore, several metabolic engineering approaches have been used to construct lactose-consuming S. cerevisiae strains, particularly involving the expression of the lactose genes of the phylogenetically related yeast Kluyveromyces lactis, but also the lactose genes from Escherichia coli and Aspergillus niger, as reviewed here. Due to the existing large amounts of whey, the production of bio-ethanol from lactose by engineered S. cerevisiae has been considered as a possible route for whey surplus. Emphasis is given in the present review on strain improvement for lactose-to-ethanol bioprocesses, namely flocculent yeast strains for continuous high-cell-density systems with enhanced ethanol productivity.
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Affiliation(s)
- Lucília Domingues
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal.
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Busti S, Sacco E, Martegani E, Vanoni M. Functional coupling of the mammalian EGF receptor to the Ras/cAMP pathway in the yeast Saccharomyces cerevisiae. Curr Genet 2008; 53:153-62. [PMID: 18183397 DOI: 10.1007/s00294-007-0173-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Revised: 12/14/2007] [Accepted: 12/15/2007] [Indexed: 01/15/2023]
Abstract
Autophosphorylation of tyrosine residues on the cytoplasmic tail of the epidermal growth factor receptor (EGFR) upon ligand binding leads to recruitment of the Grb2/Sos complex to the activated receptor and to activation of the Ras pathway. The major aim of this study was to ascertain to which extent the EGFR module (receptor, Grb2, hSos1) could work in a lower eukaryote, completely devoid of tyrosine kinase receptors but possessing hortologues to mammalian Ras proteins. We show that the EGFR module can be functionally linked to the Ras/cAMP pathway in a Saccharomyces cerevisiae cdc25 ( ts ) strain, as monitored by several independent biological readouts, including drop of budding index, decrease of cAMP level and acquisition of thermotolerance. Autophosphorylation of the receptor is a necessary step for RTK-dependent activation of the yeast Ras pathway, since genetic and pharmacological downregulation of the EGFR catalytic activity abolish coupling with the Ras/cAMP pathway. Thus, our results newly indicate that a RTK-based signal transduction module can be functionally coupled to the yeast Ras/cAMP pathway and that our system can be a valuable tool for the screen of drugs inhibiting the kinase activity of the receptor.
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Affiliation(s)
- Stefano Busti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
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Marx H, Sauer M, Resina D, Vai M, Porro D, Valero F, Ferrer P, Mattanovich D. Cloning, disruption and protein secretory phenotype of theGAS1homologue ofPichia pastoris. FEMS Microbiol Lett 2006; 264:40-7. [PMID: 17020547 DOI: 10.1111/j.1574-6968.2006.00427.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The aim of the study was the identification, cloning and disruption of the GAS1 homologue of Pichia pastoris. Gas1p is a glycoprotein anchored to the outer layer of the plasma membrane through a glycosylphosphatidylinositol (GPI) anchor. Gas1p is a beta-1,3-glucanosyltransglycosylase (EC 2.4.1.-). This cross-linking enzyme highly affects the structure and permeability of the yeast cell wall. The gene coding for the GAS1 homologue of P. pastoris was cloned by PCR, and its functionality was proven in a Saccharomyces cerevisiae GAS1 null mutant. Based on the nucleotide sequence information of the P. pastoris GAS1 homologue, a disruption cassette was constructed for the knockout of the GAS1 in P. pastoris. The morphology of DeltaGAS1 P. pastoris was identical to that of S. cerevisiae GAS1 mutants. Finally, the impact of GAS1 disruption on secretion of three recombinant model proteins in P. pastoris, human trypsinogen, human serum albumin and Rhizopus oryzae lipase, was evaluated. While the disruption had no effect on the secretion of trypsinogen and albumin, the amount of lipase released from the cells was doubled.
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Affiliation(s)
- Hans Marx
- Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
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Marx H, Sauer M, Resina D, Vai M, Porro D, Valero F, Ferrer P, Mattanovich D. Disruption of the GAS1 gene of Pichia pastoris confers a supersecretory phenotype for Rhizopus oryzae lipase, but not for human trypsinogen. Microb Cell Fact 2006. [DOI: 10.1186/1475-2859-5-s1-p69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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11
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Peres MF, Souza CS, Thomaz D, de Souza AR, Laluce C. Partitioning of the glucoamylase activity at the cell surfaces in cultures of Saccharomyces. Process Biochem 2006. [DOI: 10.1016/j.procbio.2005.01.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Branduardi P, Valli M, Brambilla L, Sauer M, Alberghina L, Porro D. The yeast Zygosaccharomyces bailii: a new host for heterologous protein production, secretion and for metabolic engineering applications. FEMS Yeast Res 2004; 4:493-504. [PMID: 14734030 DOI: 10.1016/s1567-1356(03)00200-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Molecular tools for the production of heterologous proteins and metabolic engineering applications of the non-conventional yeast Zygosaccharomyces bailii were developed. The combination of Z. bailii's resistance to relatively high temperature, osmotic pressure and low pH values, with a high specific growth rate renders this yeast potentially interesting for exploitation for biotechnological purposes as well as for the understanding of the biological phenomena and mechanisms underlying the respective resistances. Looking forward to these potential applications, here we present the tools required for the production and the secretion of different heterologous proteins, and one example of a metabolic engineering application of this non-conventional yeast, employing the newly developed molecular tools.
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Affiliation(s)
- Paola Branduardi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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Porro D, Venturini M, Brambilla L, Alberghina L, Vanoni M. Relating growth dynamics and glucoamylase excretion of individual Saccharomyces cerevisiae cells. J Microbiol Methods 2000; 42:49-55. [PMID: 11000430 DOI: 10.1016/s0167-7012(00)00171-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have developed a novel flow cytometric procedure that allows determinations of properties of protein excretion in the growth medium on a cell-by-cell basis in Saccharomyces cerevisiae. The procedure is based on labelling of a periplasmically secreted protein with antibodies conjugated to a fluorescent marker such as fluorescein isothiocyanate (FITC). The staining conditions did not perturb cell growth after resuspension of stained cells in growth medium. Decrease in fluorescence was found to correlate with excretion of glucoamylase into the growth medium. The analysis of the staining pattern over time provides information on the behaviour of individual cells belonging to different cell-cycle phases and can be used to calculate the specific excretion rate of the overall population.
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Affiliation(s)
- D Porro
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, P.zza della Scienza N degrees 2, 20126, Milan, Italy.
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