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Staudacher J, Rebnegger C, Gasser B. Treatment with surfactants enables quantification of translational activity by O-propargyl-puromycin labelling in yeast. BMC Microbiol 2021; 21:120. [PMID: 33879049 PMCID: PMC8056590 DOI: 10.1186/s12866-021-02185-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Translation is an important point of regulation in protein synthesis. However, there is a limited number of methods available to measure global translation activity in yeast. Recently, O-propargyl-puromycin (OPP) labelling has been established for mammalian cells, but unmodified yeasts are unsusceptible to puromycin. Results We could increase susceptibility by using a Komagataella phaffii strain with an impaired ergosterol pathway (erg6Δ), but translation measurements are restricted to this strain background, which displayed growth deficits. Using surfactants, specifically Imipramine, instead, proved to be more advantageous and circumvents previous restrictions. Imipramine-supplemented OPP-labelling with subsequent flow cytometry analysis, enabled us to distinguish actively translating cells from negative controls, and to clearly quantify differences in translation activities in different strains and growth conditions. Specifically, we investigated K. phaffii at different growth rates, verified that methanol feeding alters translation activity, and analysed global translation in strains with genetically modified stress response pathways. Conclusions We set up a simple protocol to measure global translation activity in yeast on a single cell basis. The use of surfactants poses a practical and non-invasive alternative to the commonly used ergosterol pathway impaired strains and thus impacts a wide range of applications where increased drug and dye uptake is needed. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02185-3.
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Affiliation(s)
- Jennifer Staudacher
- Christian Doppler Laboratory for Growth-decoupled Protein Production in Yeast, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Corinna Rebnegger
- Christian Doppler Laboratory for Growth-decoupled Protein Production in Yeast, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Brigitte Gasser
- Christian Doppler Laboratory for Growth-decoupled Protein Production in Yeast, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria. .,Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Brüning L, Raineri E, Navarro P, Bohnsack MT, Leidel SA, Díez J. A novel translational control mechanism involving RNA structures within coding sequences. Genome Res 2016; 27:95-106. [PMID: 27821408 PMCID: PMC5204348 DOI: 10.1101/gr.209015.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 11/03/2016] [Indexed: 12/20/2022]
Abstract
The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here, we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses, we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site; second, they are directly bound by Dhh1 with a specific binding distribution; and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.
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Affiliation(s)
- Jennifer Jungfleisch
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Danny D Nedialkova
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany
| | - Ivan Dotu
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Katherine E Sloan
- Institute for Molecular Biology, Göttingen University Medical Department, 37073 Göttingen, Germany
| | - Neus Martinez-Bosch
- Program of Cancer Research, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Lukas Brüning
- Institute for Molecular Biology, Göttingen University Medical Department, 37073 Göttingen, Germany
| | - Emanuele Raineri
- Statistical Genomics, Centro Nacional de Analisis Genomica, 08028 Barcelona, Spain
| | - Pilar Navarro
- Program of Cancer Research, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Markus T Bohnsack
- Institute for Molecular Biology, Göttingen University Medical Department, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, 37073 Göttingen, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany.,Faculty of Medicine, University of Münster, 48149 Münster, Germany
| | - Juana Díez
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Citterio B, Albertini MC, Ghibelli L, Falcieri E, Battistelli M, Canonico B, Rocchi MBL, Teodori L, Ciani M, Piatti E. Multiparameter analysis of apoptosis in puromycin-treated Saccharomyces cerevisiae. Arch Microbiol 2015; 197:773-80. [PMID: 25868793 DOI: 10.1007/s00203-015-1110-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 01/07/2023]
Abstract
In Saccharomyces cerevisiae, a typical apoptotic phenotype is induced by some stress factors such as sugars, acetic acid, hydrogen peroxide, aspirin and age. Nevertheless, no data have been reported for apoptosis induced by puromycin, a damaging agent known to induce apoptosis in mammalian cells. We treated S. cerevisiae with puromycin to induce apoptosis and evaluated the percentage of dead cells by using Hoechst 33342 staining, transmission electron microscopy (TEM) and Annexin V flow cytometry (FC) analysis. Hoechst 33342 fluorescence images were processed to acquire parameters to use for multiparameter analysis [and perform a principal component analysis, (PCA)]. Cell viability was evaluated by Rhodamine 123 (Rh 123) and Acridine Orange microscope fluorescence staining. The results show puromycin-induced apoptosis in S. cerevisiae, and the PCA analysis indicated that the increasing percentage of apoptotic cells delineated a well-defined graph profile. The results were supported by TEM and FC. This study gives new insights into yeast apoptosis using puromycin as inducer agent, and PCA analysis may complement molecular analysis facilitating further studies to its detection.
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Affiliation(s)
- Barbara Citterio
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
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Cary GA, Yoon SH, Torres CG, Wang K, Hays M, Ludlow C, Goodlett DR, Dudley AM. Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae. Yeast 2014; 31:167-78. [PMID: 24610064 DOI: 10.1002/yea.3007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/27/2014] [Accepted: 03/03/2014] [Indexed: 11/11/2022] Open
Abstract
Puromycin is an aminonucleoside antibiotic with structural similarity to aminoacyl tRNA. This structure allows the drug to bind the ribosomal A site and incorporate into nascent polypeptides, causing chain termination, ribosomal subunit dissociation and widespread translational arrest at high concentrations. In contrast, at sufficiently low concentrations, puromycin incorporates primarily at the C-terminus of proteins. While a number of techniques utilize puromycin incorporation as a tool for probing translational activity in vivo, these methods cannot be applied in yeasts that are insensitive to puromycin. Here, we describe a mutant strain of the yeast Saccharomyces cerevisiae that is sensitive to puromycin and characterize the cellular response to the drug. Puromycin inhibits the growth of yeast cells mutant for erg6∆, pdr1∆ and pdr3∆ (EPP) on both solid and liquid media. Puromycin also induces the aggregation of the cytoplasmic processing body component Edc3 in the mutant strain. We establish that puromycin is rapidly incorporated into yeast proteins and test the effects of puromycin on translation in vivo. This study establishes the EPP strain as a valuable tool for implementing puromycin-based assays in yeast, which will enable new avenues of inquiry into protein production and maturation.
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Affiliation(s)
- Gregory A Cary
- Institute for Systems Biology, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
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