Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization
Abstract Background Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of modera...
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | Microbial Cell Factories |
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| Online Access: | https://doi.org/10.1186/s12934-023-02074-6 |
| _version_ | 1827632648723365888 |
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| author | Marcel Albacar Abdelghani Zekhnini Jorge Pérez-Valle José L. Martínez Antonio Casamayor Joaquín Ariño |
| author_facet | Marcel Albacar Abdelghani Zekhnini Jorge Pérez-Valle José L. Martínez Antonio Casamayor Joaquín Ariño |
| author_sort | Marcel Albacar |
| collection | DOAJ |
| description | Abstract Background Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast, in search of suitable novel promoters able to drive transcription in response to the pH signal. Results In spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii. Conclusions This work defines in K. phaffii a subset of genes and diverse cellular pathways that are altered in response to moderate alkalinization of the medium, thus setting the basis for developing novel pH-controlled systems for heterologous protein expression in this fungus. |
| first_indexed | 2024-03-09T14:48:30Z |
| format | Article |
| id | doaj.art-97922fdb94e14260a3d07c0428c49e7c |
| institution | Directory Open Access Journal |
| issn | 1475-2859 |
| language | English |
| last_indexed | 2024-03-09T14:48:30Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbial Cell Factories |
| spelling | doaj.art-97922fdb94e14260a3d07c0428c49e7c2023-11-26T14:38:02ZengBMCMicrobial Cell Factories1475-28592023-04-0122111710.1186/s12934-023-02074-6Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinizationMarcel Albacar0Abdelghani Zekhnini1Jorge Pérez-Valle2José L. Martínez3Antonio Casamayor4Joaquín Ariño5Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaInstitut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaInstitut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaDepartment of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of DenmarkInstitut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaInstitut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaAbstract Background Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast, in search of suitable novel promoters able to drive transcription in response to the pH signal. Results In spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii. Conclusions This work defines in K. phaffii a subset of genes and diverse cellular pathways that are altered in response to moderate alkalinization of the medium, thus setting the basis for developing novel pH-controlled systems for heterologous protein expression in this fungus.https://doi.org/10.1186/s12934-023-02074-6Stress responseOxidative stressPromoter regulationProtein production |
| spellingShingle | Marcel Albacar Abdelghani Zekhnini Jorge Pérez-Valle José L. Martínez Antonio Casamayor Joaquín Ariño Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization Microbial Cell Factories Stress response Oxidative stress Promoter regulation Protein production |
| title | Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization |
| title_full | Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization |
| title_fullStr | Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization |
| title_full_unstemmed | Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization |
| title_short | Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization |
| title_sort | transcriptomic profiling of the yeast komagataella phaffii in response to environmental alkalinization |
| topic | Stress response Oxidative stress Promoter regulation Protein production |
| url | https://doi.org/10.1186/s12934-023-02074-6 |
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