1
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Lara AR, Utrilla J, Martínez LM, Krausch N, Kaspersetz L, Hidalgo D, Cruz-Bournazou N, Neubauer P, Sigala JC, Gosset G, Büchs J. Recombinant protein expression in proteome-reduced cells under aerobic and oxygen-limited regimes. Biotechnol Bioeng 2024; 121:1216-1230. [PMID: 38178599 DOI: 10.1002/bit.28645] [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: 05/22/2023] [Revised: 11/18/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
Industrial cultures are hindered by the physiological complexity of the host and the limited mass transfer capacity of conventional bioreactors. In this study, a minimal cell approach was combined with genetic devices to overcome such issues. A flavin mononucleotide-based fluorescent protein (FbFP) was expressed in a proteome-reduced Escherichia coli (PR). When FbFP was expressed from a constitutive protein generator (CPG), the PR strain produced 47% and 35% more FbFP than its wild type (WT), in aerobic or oxygen-limited regimes, respectively. Metabolic and expression models predicted more efficient biomass formation at higher fluxes to FbFP, in agreement with these results. A microaerobic protein generator (MPG) and a microaerobic transcriptional cascade (MTC) were designed to induce FbFP expression upon oxygen depletion. The FbFP fluorescence using the MTC in the PR strain was 9% higher than that of the WT bearing the CPG under oxygen limitation. To further improve the PR strain, the pyruvate dehydrogenase complex regulator gene was deleted, and the Vitreoscilla hemoglobin was expressed. Compared to oxygen-limited cultures of the WT, the engineered strains increased the FbFP expression more than 50% using the MTC. Therefore, the designed expression systems can be a valuable alternative for industrial cultivations.
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Affiliation(s)
- Alvaro R Lara
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Jose Utrilla
- Synthetic Biology Program, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Luz María Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Niels Krausch
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Lucas Kaspersetz
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - David Hidalgo
- Synthetic Biology Program, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
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2
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Zhou H, Wang Z, Qian J. Engineering of the hypoxia-induced Pichia stipitis ADH2 promoter to construct a promoter library for Pichia pastoris. J Biotechnol 2023; 376:24-32. [PMID: 37690664 DOI: 10.1016/j.jbiotec.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Hypoxia-inducible promoters of a wide range of activities are desirable for fine-tuning gene expression in response to oxygen limitation, especially for the Crabtree negative yeast Pichia pastoris (Komagataella phaffii) with a high oxygen consumption rate in large-scale fermentations. Here we constructed a hypoxia-inducible promoter library for P. pastoris through error-prone PCR of Pichia stipitis ADH2 promoter (PsADH2). The library of 30 selected promoters showing 0.4- to 5.5-fold of the PsADH2 activity was obtained through high-throughput screening in microplates using the reporter yeast-enhanced green fluorescent protein. Two strong promoters, AM23 and AM30, were further characterized in shake flask cultures at high and low dissolved oxygen levels. They responded more sensitively to the low dissolved oxygen level, achieving a 4.6-, 7.9-fold and 3.6-, 7.7-fold higher fluorescence intensity and transcript level, respectively, than the wild-type PsADH2. Their hypoxia-inducible properties were confirmed with two additional reporters: β-galactosidase and Vitreoscilla hemoglobin, to demonstrate the broad applicability of the promoter library. During the typical fermentation process in shake flasks, the promoter AM30 showed strong expression with cell growth and decreased oxygen levels, without any additional chemical inducers or operations. Since the potent industrial host P. pastoris is recognized as an easy to scale-up system, it is reasonable to expect that the obtained hypoxia-inducible promoter library may have great potential to enable convenient regulation of gene expression under industrial fermentations which are usually run under oxygen limitation due to high cell density cultivations.
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Affiliation(s)
- Hangcheng Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Zhipeng Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Jiangchao Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China.
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3
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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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4
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Chen X, Li C, Liu H. Enhanced Recombinant Protein Production Under Special Environmental Stress. Front Microbiol 2021; 12:630814. [PMID: 33935992 PMCID: PMC8084102 DOI: 10.3389/fmicb.2021.630814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/19/2021] [Indexed: 01/09/2023] Open
Abstract
Regardless of bacteria or eukaryotic microorganism hosts, improving their ability to express heterologous proteins is always a goal worthy of elaborate study. In addition to traditional methods including intracellular synthesis process regulation and extracellular environment optimization, some special or extreme conditions can also be employed to create an enhancing effect on heterologous protein production. In this review, we summarize some extreme environmental factors used for the improvement of heterologous protein expression, including low temperature, hypoxia, microgravity and high osmolality. The applications of these strategies are elaborated with examples of well-documented studies. We also demonstrated the confirmed or hypothetical mechanisms of environment stress affecting the host behaviors. In addition, multi-omics techniques driving the stress-responsive research for construction of efficient microbial cell factories are also prospected at the end.
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Affiliation(s)
- Xinyi Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Hu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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5
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Santomartino R, Ottaviano D, Camponeschi I, Landicho TAA, Falato L, Visca A, Soulard A, Lemaire M, Bianchi MM. The hypoxic expression of the glucose transporter RAG1 reveals the role of the bHLH transcription factor Sck1 as a novel hypoxic modulator in Kluyveromyces lactis. FEMS Yeast Res 2020; 19:5519861. [PMID: 31210264 DOI: 10.1093/femsyr/foz041] [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: 12/10/2018] [Accepted: 06/16/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is the preferred nutrient for most living cells and is also a signaling molecule that modulates several cellular processes. Glucose regulates the expression of glucose permease genes in yeasts through signaling pathways dependent on plasma membrane glucose sensors. In the yeast Kluyveromyces lactis, sufficient levels of glucose induction of the low-affinity glucose transporter RAG1 gene also depends on a functional glycolysis, suggesting additional intracellular signaling. We have found that the expression of RAG1 gene is also induced by hypoxia in the presence of glucose, indicating that glucose and oxygen signaling pathways are interconnected. In this study we investigated the molecular mechanisms underlying this crosstalk. By analyzing RAG1 expression in various K. lactis mutants, we found that the bHLH transcriptional activator Sck1 is required for the hypoxic induction of RAG1 gene. The RAG1 promoter region essential for its hypoxic induction was identified by promoter deletion experiments. Taken together, these results show that the RAG1 glucose permease gene is synergistically induced by hypoxia and glucose and highlighted a novel role for the transcriptional activator Sck1 as a key mediator in this mechanism.
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Affiliation(s)
- Rosa Santomartino
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Ottaviano
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Ilaria Camponeschi
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | | | - Luca Falato
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Visca
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Alexandre Soulard
- Université Lyon 1, CNRS, INSA de Lyon, UMR5240 Microbiologie, Adaptation et Pathogénie, Génétique Moléculaire des Levures, Villeurbanne F69622, France
| | - Marc Lemaire
- Université Lyon 1, CNRS, INSA de Lyon, UMR5240 Microbiologie, Adaptation et Pathogénie, Génétique Moléculaire des Levures, Villeurbanne F69622, France
| | - Michele Maria Bianchi
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
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6
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Gündüz Ergün B, Hüccetoğulları D, Öztürk S, Çelik E, Çalık P. Established and Upcoming Yeast Expression Systems. Methods Mol Biol 2019; 1923:1-74. [PMID: 30737734 DOI: 10.1007/978-1-4939-9024-5_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.
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Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Damla Hüccetoğulları
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Sibel Öztürk
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Bioengineering Division, Institute of Science, Hacettepe University, Ankara, Turkey
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey.
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, Turkey.
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7
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Bonanomi M, Roffia V, De Palma A, Lombardi A, Aprile FA, Visentin C, Tortora P, Mauri P, Regonesi ME. The polyglutamine protein ataxin-3 enables normal growth under heat shock conditions in the methylotrophic yeast Pichia pastoris. Sci Rep 2017; 7:13417. [PMID: 29042637 PMCID: PMC5645362 DOI: 10.1038/s41598-017-13814-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/12/2017] [Indexed: 11/11/2022] Open
Abstract
The protein ataxin-3 carries a polyglutamine stretch close to the C-terminus that triggers a neurodegenerative disease in humans when its length exceeds a critical threshold. A role as a transcriptional regulator but also as a ubiquitin hydrolase has been proposed for this protein. Here, we report that, when expressed in the yeast Pichia pastoris, full-length ataxin-3 enabled almost normal growth at 37 °C, well above the physiological optimum of 30 °C. The N-terminal Josephin domain (JD) was also effective but significantly less, whereas catalytically inactive JD was completely ineffective. Based on MudPIT proteomic analysis, we observed that the strain expressing full-length, functional ataxin-3 displayed persistent upregulation of enzymes involved in mitochondrial energy metabolism during growth at 37 °C compared with the strain transformed with the empty vector. Concurrently, in the transformed strain intracellular ATP levels at 37 °C were even higher than normal ones at 30 °C. Elevated ATP was also paralleled by upregulation of enzymes involved in both protein biosynthesis and biosynthetic pathways, as well as of several stress-induced proteins. A similar pattern was observed when comparing a strain expressing JD with another expressing its catalytically inactive counterpart. We suggest that such effects mostly result from mechanisms of transcriptional regulation.
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Affiliation(s)
- Marcella Bonanomi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy.,SYSBIO.IT, Centre of Systems Biology, 20126, Milano, Italy
| | - Valentina Roffia
- Institute for Biomedical Technologies, National Research Council, 20090, Milan, Italy
| | - Antonella De Palma
- Institute for Biomedical Technologies, National Research Council, 20090, Milan, Italy
| | - Alessio Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | | | - Cristina Visentin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy. .,Milan Center of Neuroscience (NeuroMI), 20126, Milano, Italy.
| | - Pierluigi Mauri
- Institute for Biomedical Technologies, National Research Council, 20090, Milan, Italy.
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy.,Milan Center of Neuroscience (NeuroMI), 20126, Milano, Italy
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8
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Kuanyshev N, Adamo GM, Porro D, Branduardi P. The spoilage yeastZygosaccharomyces bailii: Foe or friend? Yeast 2017; 34:359-370. [DOI: 10.1002/yea.3238] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nurzhan Kuanyshev
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Giusy M. Adamo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
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9
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Abstract
Laccases are multi-copper oxidoreductases which catalyze the oxidation of a wide range of substrates during the simultaneous reduction of oxygen to water. These enzymes, originally found in fungi, plants, and other natural sources, have many industrial and biotechnological applications. They are used in the food, textile, pulp, and paper industries, as well as for bioremediation purposes. Although natural hosts can provide relatively high levels of active laccases after production optimization, heterologous expression can bring, moreover, engineered enzymes with desired properties, such as different substrate specificity or improved stability. Hence, diverse hosts suitable for laccase production are reviewed here, while the greatest emphasis is placed on yeasts which are commonly used for industrial production of various proteins. Different approaches to optimize the laccase expression and activity are also discussed in detail here.
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Affiliation(s)
- Zuzana Antošová
- Department of Membrane Transport, Institute of Physiology, Czech Academy of Sciences (CAS), Vídeňská 1083, 142 20, Prague 4, Czech Republic.
| | - Hana Sychrová
- Department of Membrane Transport, Institute of Physiology, Czech Academy of Sciences (CAS), Vídeňská 1083, 142 20, Prague 4, Czech Republic.
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10
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Homologous and Heterologous Expression of Basidiomycete Genes Related to Plant Biomass Degradation. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Çalık P, Ata Ö, Güneş H, Massahi A, Boy E, Keskin A, Öztürk S, Zerze GH, Özdamar TH. Recombinant protein production in Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter: From carbon source metabolism to bioreactor operation parameters. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Landi C, Paciello L, de Alteriis E, Brambilla L, Parascandola P. High cell density culture with S. cerevisiae CEN.PK113-5D for IL-1β production: optimization, modeling, and physiological aspects. Bioprocess Biosyst Eng 2014; 38:251-61. [PMID: 25106469 DOI: 10.1007/s00449-014-1264-8] [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] [Received: 04/24/2014] [Accepted: 07/29/2014] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae CEN.PK113-5D, a strain auxotrophic for uracil belonging to the CEN.PK family of the yeast S. cerevisiae, was cultured in aerated fed-batch reactor as such and once transformed to express human interleukin-1β (IL-1β), aiming at obtaining high cell densities and optimizing IL-1β production. Three different exponentially increasing glucose feeding profiles were tested, all of them "in theory" promoting respiratory metabolism to obtain high biomass/product yield. A non-structured non-segregated model was developed to describe the performance of S. cerevisiae CEN.PK113-5D during the fed-batch process and, in particular, its capability to metabolize simultaneously glucose and ethanol which derived from the precedent batch growth. Our study showed that the proliferative capacity of the yeast population declined along the fed-batch run, as shown by the exponentially decreasing specific growth rates on glucose. Further, a shift towards fermentative metabolism occurred. This shift took place earlier the higher was the feed rate and was more pronounced in the case of the recombinant strain. Determination of some physiological markers (acetate production, intracellular ROS accumulation, catalase activity and cell viability) showed that neither poor oxygenation nor oxidative stress was responsible for the decreased specific growth rate, nor for the shift to fermentative metabolism.
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Affiliation(s)
- Carmine Landi
- Dep. Ingegneria Industriale, Università Di Salerno, Via Giovanni Paolo II, 132 Fisciano, 84084, Salerno, Italy
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13
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Ottaviano D, Micolonghi C, Tizzani L, Lemaire M, Wésolowski-Louvel M, De Stefano ME, Ranieri D, Bianchi MM. Autoregulation of the Kluyveromyces lactis pyruvate decarboxylase gene KlPDC1 involves the regulatory gene RAG3. MICROBIOLOGY-SGM 2014; 160:1369-1378. [PMID: 24763423 DOI: 10.1099/mic.0.078543-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the yeast Kluyveromyces lactis, the pyruvate decarboxylase gene KlPDC1 is strongly regulated at the transcription level by different environmental factors. Sugars and hypoxia act as inducers of transcription, while ethanol acts as a repressor. Their effects are mediated by gene products, some of which have been characterized. KlPDC1 transcription is also strongly repressed by its product--KlPdc1--through a mechanism called autoregulation. We performed a genetic screen that allowed us to select and identify the regulatory gene RAG3 as a major factor in the transcriptional activity of the KlPDC1 promoter in the absence of the KlPdc1 protein, i.e. in the autoregulatory mechanism. We also showed that the two proteins Rag3 and KlPdc1 interact, co-localize in the cell and that KlPdc1 may control Rag3 nuclear localization.
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Affiliation(s)
- Daniela Ottaviano
- Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Chiara Micolonghi
- Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Lorenza Tizzani
- Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Marc Lemaire
- CNRS, Villeurbanne, France.,Université Lyon1, Lyon, France.,Génétique Moléculaire des Levures, UMR5240 Microbiologie, Adaptation et Pathogénie, Université de Lyon, Lyon, France
| | - Micheline Wésolowski-Louvel
- CNRS, Villeurbanne, France.,Université Lyon1, Lyon, France.,Génétique Moléculaire des Levures, UMR5240 Microbiologie, Adaptation et Pathogénie, Université de Lyon, Lyon, France
| | - Maria Egle De Stefano
- Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy.,Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Danilo Ranieri
- Dip. Medicina clinica e molecolare, Sapienza Università di Roma, via di Grottarossa 1035, 00189 Roma, Italy
| | - Michele M Bianchi
- Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy.,Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
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14
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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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15
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Rivera-Hoyos CM, Morales-Álvarez ED, Poutou-Piñales RA, Pedroza-Rodríguez AM, RodrÍguez-Vázquez R, Delgado-Boada JM. Fungal laccases. FUNGAL BIOL REV 2013. [DOI: 10.1016/j.fbr.2013.07.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Production of recombinant proteins by yeast cells. Biotechnol Adv 2012; 30:1108-18. [DOI: 10.1016/j.biotechadv.2011.09.011] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/12/2011] [Accepted: 09/17/2011] [Indexed: 01/14/2023]
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Kluyveromyces lactis: a suitable yeast model to study cellular defense mechanisms against hypoxia-induced oxidative stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:634674. [PMID: 22928082 PMCID: PMC3425888 DOI: 10.1155/2012/634674] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/22/2012] [Indexed: 11/17/2022]
Abstract
Studies about hypoxia-induced oxidative stress in human health disorders take advantage from the use of unicellular eukaryote models. A widely extended model is the fermentative yeast Saccharomyces cerevisiae. In this paper, we describe an overview of the molecular mechanisms induced by a decrease in oxygen availability and their interrelationship with the oxidative stress response in yeast. We focus on the differential characteristics between S. cerevisiae and the respiratory yeast Kluyveromyces lactis, a complementary emerging model, in reference to multicellular eukaryotes.
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Micolonghi C, Ottaviano D, Di Silvio E, Damato G, Heipieper HJ, Bianchi MM. A dual signalling pathway for the hypoxic expression of lipid genes, dependent on the glucose sensor Rag4, is revealed by the analysis of the KlMGA2 gene in Kluyveromyces lactis. MICROBIOLOGY-SGM 2012; 158:1734-1744. [PMID: 22516223 DOI: 10.1099/mic.0.059402-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the respiratory yeast Kluyveromyces lactis, little is known about the factors regulating the metabolic response to oxygen shortage. After searching for homologues of characterized Saccharomyces cerevisiae regulators of the hypoxic response, we identified a gene that we named KlMGA2, which is homologous to MGA2. The deletion of KlMGA2 strongly reduced both the fermentative and respiratory growth rate and altered fatty acid composition and the unsaturation index of membranes. The reciprocal heterologous expression of MGA2 and KlMGA2 in the corresponding deletion mutant strains suggested that Mga2 and KlMga2 are functional homologues. KlMGA2 transcription was induced by hypoxia and the glucose sensor Rag4 mediated the hypoxic induction of KlMGA2. Transcription of lipid biosynthetic genes KlOLE1, KlERG1, KlFAS1 and KlATF1 was induced by hypoxia and was dependent on KlMga2, except for KlOLE1. Rag4 was required for hypoxic induction of transcription for both KlMga2-dependent (KlERG1) and KlMga2-independent (KlOLE1) structural genes.
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Affiliation(s)
- Chiara Micolonghi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Ottaviano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Eva Di Silvio
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Giuseppe Damato
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Michele M Bianchi
- Pasteur Institut Cenci-Bolognetti Foundation, Sapienza University of Rome, Italy.,Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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Piscitelli A, Pezzella C, Giardina P, Faraco V, Giovanni S. Heterologous laccase production and its role in industrial applications. Bioeng Bugs 2011; 1:252-62. [PMID: 21327057 DOI: 10.4161/bbug.1.4.11438] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/25/2010] [Accepted: 01/27/2010] [Indexed: 02/04/2023] Open
Abstract
Laccases are blue multicopper oxidases, catalyzing the oxidation of an array of aromatic substrates concomitantly with the reduction of molecular oxygen to water. These enzymes are implicated in a variety of biological activities. Most of the laccases studied thus far are of fungal origin. The large range of substrates oxidized by laccases has raised interest in using them within different industrial fields, such as pulp delignification, textile dye bleaching, and bioremediation. Laccases secreted from native sources are usually not suitable for large-scale purposes, mainly due to low production yields and high cost of preparation/purification procedures. Heterologous expression may provide higher enzyme yields and may permit to produce laccases with desired properties (such as different substrate specificities, or improved stabilities) for industrial applications. This review surveys researches on heterologous laccase expression focusing on the pivotal role played by recombinant systems towards the development of robust tools for greening modern industry.
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Affiliation(s)
- Alessandra Piscitelli
- Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte S. Angelo, Napoli, Italy.
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The Rag4 glucose sensor is involved in the hypoxic induction of KlPDC1 gene expression in the yeast Kluyveromyces lactis. EUKARYOTIC CELL 2010; 10:146-8. [PMID: 21097667 DOI: 10.1128/ec.00251-10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Kluyveromyces lactis is a yeast which cannot grow under strict anaerobiosis. To date, no factors responsible for oxygen sensing and oxygen-dependent regulation of metabolism have been identified. In this paper we present the identification of the glucose sensor Rag4 as a factor essential for oxygen-dependent regulation of the fermentative pathway.
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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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Cloning of the Zygosaccharomyces bailii GAS1 homologue and effect of cell wall engineering on protein secretory phenotype. Microb Cell Fact 2010; 9:7. [PMID: 20102600 PMCID: PMC2825207 DOI: 10.1186/1475-2859-9-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 01/26/2010] [Indexed: 11/23/2022] Open
Abstract
Background Zygosaccharomyces bailii is a diploid budding yeast still poorly characterized, but widely recognised as tolerant to several stresses, most of which related to industrial processes of production. Because of that, it would be very interesting to develop its ability as a cell factory. Gas1p is a β-1,3-glucanosyltransglycosylase which plays an important role in cell wall construction and in determining its permeability. Cell wall defective mutants of Saccharomyces cerevisiae and Pichia pastoris, deleted in the GAS1 gene, were reported as super-secretive. The aim of this study was the cloning and deletion of the GAS1 homologue of Z. bailii and the evaluation of its deletion on recombinant protein secretion. Results The GAS1 homologue of Z. bailii was cloned by PCR, and when expressed in a S. cerevisiae GAS1 null mutant was able to restore the parental phenotype. The respective Z. bailii Δgas1 deleted strain was obtained by targeted deletion of both alleles of the ZbGAS1 gene with deletion cassettes having flanking regions of ~400 bp. The morphological and physiological characterization of the Z. bailii null mutant resulted very similar to that of the corresponding S. cerevisiae mutant. As for S. cerevisiae, in the Z. bailii Δgas1 the total amount of protein released in the medium was significantly higher. Moreover, three different heterologous proteins were expressed and secreted in said mutant. The amount of enzymatic activity found in the medium was almost doubled in the case of the Candida rugosa lipase CRL1 and of the Yarrowia lipolytica protease XPR2, while for human IL-1β secretion disruption had no relevant effect. Conclusions The data presented confirm that the engineering of the cell wall is an effective way to improve protein secretion in yeast. They also confirmed that Z. bailii is an interesting candidate, despite the knowledge of its genome and the tools for its manipulation still need to be improved. However, as already widely reported in literature, our data confirmed that an "always working" solution to the problems related to recombinant protein production can be hardly, if never, found; instead, manipulations have to be finely tuned for each specific product and/or combination of host cell and product.
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Ranieri D, Colao MC, Ruzzi M, Romagnoli G, Bianchi MM. Optimization of recombinant fungal laccase production with strains of the yeastKluyveromyces lactisâfrom the pyruvate decarboxylase promoter. FEMS Yeast Res 2009; 9:892-902. [DOI: 10.1111/j.1567-1364.2009.00532.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Kunamneni A, Camarero S, García-Burgos C, Plou FJ, Ballesteros A, Alcalde M. Engineering and Applications of fungal laccases for organic synthesis. Microb Cell Fact 2008; 7:32. [PMID: 19019256 PMCID: PMC2613868 DOI: 10.1186/1475-2859-7-32] [Citation(s) in RCA: 199] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 11/20/2008] [Indexed: 11/10/2022] Open
Abstract
Laccases are multi-copper containing oxidases (EC 1.10.3.2), widely distributed in fungi, higher plants and bacteria. Laccase catalyses the oxidation of phenols, polyphenols and anilines by one-electron abstraction, with the concomitant reduction of oxygen to water in a four-electron transfer process. In the presence of small redox mediators, laccase offers a broader repertory of oxidations including non-phenolic substrates. Hence, fungal laccases are considered as ideal green catalysts of great biotechnological impact due to their few requirements (they only require air, and they produce water as the only by-product) and their broad substrate specificity, including direct bioelectrocatalysis. Thus, laccases and/or laccase-mediator systems find potential applications in bioremediation, paper pulp bleaching, finishing of textiles, bio-fuel cells and more. Significantly, laccases can be used in organic synthesis, as they can perform exquisite transformations ranging from the oxidation of functional groups to the heteromolecular coupling for production of new antibiotics derivatives, or the catalysis of key steps in the synthesis of complex natural products. In this review, the application of fungal laccases and their engineering by rational design and directed evolution for organic synthesis purposes are discussed.
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Affiliation(s)
- Adinarayana Kunamneni
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, CSIC, Marie Curie 2, 28049 Madrid, Spain.
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Dato L, Sauer M, Passolunghi S, Porro D, Branduardi P. Investigating the multibudded and binucleate phenotype ofâ the yeastZygosaccharomyces bailiigrowing on minimal medium. FEMS Yeast Res 2008; 8:906-15. [DOI: 10.1111/j.1567-1364.2008.00417.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Maya D, Quintero MJ, de la Cruz Muñoz-Centeno M, Chávez S. Systems for applied gene control in Saccharomyces cerevisiae. Biotechnol Lett 2008; 30:979-87. [DOI: 10.1007/s10529-008-9647-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 01/14/2008] [Accepted: 01/17/2008] [Indexed: 01/06/2023]
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Goh S, Camattari A, Ng D, Song R, Madden K, Westpheling J, Wong VVT. An integrative expression vector for Actinosynnema pretiosum. BMC Biotechnol 2007; 7:72. [PMID: 17956638 PMCID: PMC2194683 DOI: 10.1186/1472-6750-7-72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 10/24/2007] [Indexed: 11/10/2022] Open
Abstract
Background The Actinomycete Actinosynnema pretiosum ssp. auranticum has commercial importance due to its production of ansamitocin P-3 (AP-3), a potent antitumor agent. One way to increase AP-3 production would be to constitutively express selected genes so as to relieve bottlenecks in the biosynthetic pathway; however, an integrative expression vector for A. pretiosum is lacking. The aim of this study was to construct a vector for heterologous gene expression in A. pretiosum. Results A series of integrative expression vectors have been made with the following features: the IS117 transposase from Streptomyces coelicolor, the constitutive ermE* promoter from Saccharopolyspora erythraea, different ribosome-binding site (RBS) sequences and xylE as a translational reporter. Positive E. coli clones and A. pretiosum transconjugants were assayed by catechol. pAP42, containing an E. coli consensus RBS, and pAP43, containing an asm19 RBS, gave strong and moderate gene expression, respectively. In addition, an operon construct capable of multi-gene expression was created. Plasmid integration sites in transconjugants were investigated and four different sites were observed. Although the most common integration site was within a putative ORF with sequence similarity to NADH-flavin reductase, AP-3 levels and cell growth of transconjugants were unaffected. Conclusion A set of integrative vectors for constitutive gene expression in A. pretiosum has been constructed. Gene translation is easily determined by colorimetric assay on an agar plate. The vectors are suitable for studies relating to AP-3 biosynthesis as they do not affect AP-3 production.
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Affiliation(s)
- Shan Goh
- Bioprocessing Technology Institute, 20 Biopolis Way, Centros #06-01, Singapore.
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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